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Alcolea-Medina A, Fernandez MTC, Montiel N, García MPL, Sevilla CD, North N, Lirola MJM, Wilks M. An improved simple method for the identification of Mycobacteria by MALDI-TOF MS (Matrix-Assisted Laser Desorption- Ionization mass spectrometry). Sci Rep 2019; 9:20216. [PMID: 31882826 PMCID: PMC6934676 DOI: 10.1038/s41598-019-56604-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/06/2019] [Indexed: 12/30/2022] Open
Abstract
The aim of this study was to establish a simple method for the rapid identification of Mycobacteria species by MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass spectrometry) using the Bruker MALDI-TOF Biotyper system (Bruker Daltonik, Bremen, Germany). A multicentre, prospective, and single blind study was performed in three European Hospitals, two Spanish and one UK hospital from May to August 2018. The BD BACTEC MGIT (Becton Dickinson, Berks, UK) liquid culture system was used in all three centres for the growth of Mycobacteria. When signal positive, tubes were removed from the analyser and in addition to standard laboratory procedures were subcultured on blood agar plates for MALDI-TOF analysis. Plates were incubated aerobically for 1 to 7 days at 37 °C and inspected every day. Once any growth was visible, it was transferred to the steel target plate, overlaid with 1 μl of neat formic acid and 1 μl HCCA matrix (alpha hydroxyl 4 cinnamic acid), and analysed in a Bruker Biotyper MALDI-TOF. Results given by MALDI-TOF were compared with the reference methods used for identification in the different centres. At two Spanish hospitals, identification by MALDI-TOF was only attempted on presumptive non-tuberculosis mycobacteria (NTM) and the results were initially compared with the results obtained by a commercial reverse hybridisation assay, GenoType CM/AS (Hain Lifescience, Tübingen, Germany). At the UK Hospital, identification of any presumptive mycobacteria was attempted and compared with the results obtained by whole genome sequencing (WGS). Overall in 142/167 (85%) of cases the identifications obtained were concordant; all Mycobacterium tuberculosis (MTB) isolates 43/43 (100%), 57/76 (75%) of the rapid growing nontuberculous mycobacteria (NTM), and 42/48 (85%) slow growing NTM tested were identified correctly. We report a new, easy, cheap and quick method for isolation and identification of Mycobacterium spp. without the need for additional steps or equipment and this method is in routine used in all three centres.
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Affiliation(s)
- Adela Alcolea-Medina
- Microbiology, Division of Infection, Barts Health NHS Trust, 80 Newark St, E1 2ES, London, UK
| | - M T Cabezas Fernandez
- C.H.U. Torrecárdenas Almería, Calle Hermandad de Donantes de Sangre, s/n, 04009, Almería, Spain
| | - N Montiel
- A.S.H. Costa del Sol, Málaga A-7, Km 187, 29603, Marbella, Málaga, Spain
| | | | - C Delamo Sevilla
- C.H.U. Torrecárdenas Almería, Calle Hermandad de Donantes de Sangre, s/n, 04009, Almería, Spain
| | - Nathan North
- Microbiology, Division of Infection, Barts Health NHS Trust, 80 Newark St, E1 2ES, London, UK
| | - M J Martínez Lirola
- C.H.U. Torrecárdenas Almería, Calle Hermandad de Donantes de Sangre, s/n, 04009, Almería, Spain
| | - Mark Wilks
- Microbiology, Division of Infection, Barts Health NHS Trust, 80 Newark St, E1 2ES, London, UK. .,Immunobiology, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary, University of London, London, UK.
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Huh HJ, Kim SY, Jhun BW, Shin SJ, Koh WJ. Recent advances in molecular diagnostics and understanding mechanisms of drug resistance in nontuberculous mycobacterial diseases. INFECTION GENETICS AND EVOLUTION 2018; 72:169-182. [PMID: 30315892 DOI: 10.1016/j.meegid.2018.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 01/31/2023]
Abstract
Accumulating evidence suggests that human infections caused by nontuberculous mycobacteria (NTM) are increasing worldwide, indicating that NTM disease is no longer uncommon in many countries. As a result of an increasing emphasis on the importance of differential identification of NTM species, several molecular tools have recently been introduced in clinical and experimental settings. These advances have led to a much better understanding of the diversity of NTM species with regard to clinical aspects and the potential factors responsible for drug resistance that influence the different outcomes of NTM disease. In this paper, we review currently available molecular diagnostics for identification and differentiation of NTM species by summarizing data from recently applied methods, including commercially available assays, and their relevant strengths and weaknesses. We also highlight drug resistance-associated genes in clinically important NTM species. Understanding the basis for different treatment outcomes with different causative species and drug-resistance mechanisms will eventually improve current treatment regimens and facilitate the development of better control measures for NTM diseases.
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Affiliation(s)
- Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
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Ustinova VV, Smirnova TG, Sochivko DG, Varlamov DA, Larionova EE, Andreevskaya SN, Andrievskaya IY, Kiseleva EA, Chernousova LN, Ergeshov A. New assay to diagnose and differentiate between Mycobacterium tuberculosis complex and nontuberculous mycobacteria. Tuberculosis (Edinb) 2018; 114:17-23. [PMID: 30711153 DOI: 10.1016/j.tube.2018.10.004] [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: 03/28/2018] [Revised: 10/02/2018] [Accepted: 10/07/2018] [Indexed: 11/29/2022]
Abstract
The purpose of the present study was to create a real-time PCR test system allowing simultaneous detection of nontuberculous mycobacteria (NTM) and Mycobacterium tuberculosis complex (MTBC) both in culture and sputum. NTM cultures (18 strains, 18 species), MTBC cultures (16 strains, 2 species) and non-mycobacterial microorganisms from the collection of the Central Research TB Institute (CTRI) were used for the preliminary evaluation of the test system. 301 NTM cultures from patients with mycobacteriosis were used to assess the sensitivity of the developed test system. Clinical respiratory samples (sputum) from 104 patients with mycobacteriosis, 3627 patients with tuberculosis and 118 patients with other lung diseases were used for diagnostic sensitivity and specificity testing. The specificity and sensitivity of the assay for MTBC was found to be 100% both in culture and sputum samples; for NTM, the specificity was 100% in culture and sputum, the sensitivity reached 100% in culture and 73.1% in sputum samples. Positive predictive value (PPV) and negative predictive value (NPV) of the assay for culture were both 100%, for clinical material 100% and 80.8%, respectively. The limit of detection at the probability of detection 95% (LoD95%) was estimated to be 16 cfu/ml for M. tuberculosis H37RV and 1200 cfu/ml for M. avium.
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Affiliation(s)
- Vera V Ustinova
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia.
| | - Tatiana G Smirnova
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
| | | | - Dmitry A Varlamov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | - Elena E Larionova
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
| | - Sofya N Andreevskaya
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
| | - Irina Yu Andrievskaya
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
| | - Ekaterina A Kiseleva
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
| | - Larisa N Chernousova
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
| | - Atadzhan Ergeshov
- Microbiology Department, Central Tuberculosis Research Institute RAMS, Moscow, Russia
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Abstract
ABSTRACT
The immunocompromised host is at increased risk of
Mycobacterium tuberculosis
complex and nontuberculous mycobacteria infection. Although
Mycobacterium tuberculosis
complex is a significant mycobacterial pathogen, nontuberculous mycobacteria causes substantial disease in those with suppressed immune responses. Mycobacterial infections can cause significant morbidity and mortality in this patient population, and rapid identification and susceptibility testing of the mycobacterial species is paramount to patient management and outcomes. Mycobacterial diagnostics has undergone some significant advances in the last two decades with immunodiagnostics (interferon gamma release assay), microscopy (light-emitting diode), culture (automated broth-based systems), identification (direct PCR, sequencing and matrix-assisted laser-desorption ionization–time of flight mass spectrometry) and susceptibility testing (molecular detection of drug resistance from direct specimens or positive cultures). Employing the most rapid and sensitive methods in the mycobacterial laboratory will have a tremendous impact on patient care and, in the case of
Mycobacterium tuberculosis
complex, in the control of tuberculosis.
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Nagai S, Miyamoto S, Ino K, Tajimi S, Nishi H, Tomono J. Easy detection of multiple Alexandrium species using DNA chromatography chip. HARMFUL ALGAE 2016; 51:97-106. [PMID: 28003065 DOI: 10.1016/j.hal.2015.10.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Revised: 10/17/2015] [Accepted: 10/24/2015] [Indexed: 06/06/2023]
Abstract
In this study, the Kaneka DNA chromatography chip (KDCC) for the Alexandrium species was successfully developed for simultaneous detection of five Alexandrium species. This method utilizes a DNA-DNA hybridization technology. In the PCR process, specifically designed tagged-primers are used, i.e. a forward primer consisting of a tag domain, which can conjugate with gold nanocolloids on the chip, and a primer domain, which can anneal/amplify the target sequence. However, the reverse primer consists of a tag domain, which can hybridize to the solid-phased capture probe on the chip, and a primer domain, which can anneal/amplify the target sequence. As a result, a red line that originates from gold nanocolloids appears as a positive signal on the chip, and the amplicon is detected visually by the naked eye. This technique is simple, because it is possible to visually detect the target species soon after (<5min) the application of 2μL of PCR amplicon and 65μL of development buffer to the sample pad of the chip. Further, this technique is relatively inexpensive and does not require expensive laboratory equipment, such as real-time Q-PCR machines or DNA microarray detectors, but a thermal cycler. Regarding the detection limit of KDCC for the five Alexandrium species, it varied among species and it was <0.1-10pg and equivalent to 5-500 copies of rRNA genes, indicating that the technique is sensitive enough for practical use to detect several cells of the target species from 1L of seawater. The detection sensitivity of KDCC was also evaluated with two different techniques, i.e. a multiplex-PCR and a digital DNA hybridization by digital DNA chip analyzer (DDCA), using natural plankton assemblages. There was no significant difference in the detection sensitivity among the three techniques, suggesting KDCC can be readily used to monitor the HAB species.
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Affiliation(s)
- Satoshi Nagai
- National Research Institute of Fisheries Science, Research Center for Aquatic Genomics, 2-12-4 Fukuura, Kanazawa-ku, Yokohama 236-8648, Kanagawa, Japan.
| | - Shigehiko Miyamoto
- Kaneka Corporation, Medical Device Development Laboratories, 1-8 Mayamae-cho, Takasago 676-8688, Hyogo, Japan
| | - Keita Ino
- Kaneka Corporation, Medical Device Development Laboratories, 1-8 Mayamae-cho, Takasago 676-8688, Hyogo, Japan
| | - Seisuke Tajimi
- Kumamoto Prefectural Fisheries Research Center, 2450-2 Naka, Oyano-machi, Kami-amakusa 869-3603, Kumamoto, Japan
| | - Hiromi Nishi
- Kagoshima Prefectural Fisheries Technology and Development Center, 160-10 Takadaue, Iwamoto, Ibusuki 891-0315, Kagoshima, Japan
| | - Jun Tomono
- Kaneka Corporation, Medical Device Development Laboratories, 1-8 Mayamae-cho, Takasago 676-8688, Hyogo, Japan
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Ramis IB, Cnockaert M, Von Groll A, Mathys V, Simon A, Tortoli E, Palomino JC, Almeida da Silva PE, Vandamme P, Andre E, Martin A. Evaluation of the Speed-Oligo Mycobacteria assay for the identification of nontuberculous mycobacteria. J Med Microbiol 2015; 64:283-287. [PMID: 25596120 DOI: 10.1099/jmm.0.000025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) causing human infectious disease have become increasingly common. Rapid and accurate identification to the species level is, therefore, critical. The Speed-Oligo Mycobacteria assay is an oligochromatographic method that was made available recently for the identification and differentiation of mycobacteria. The present study aimed to evaluate the performance of the Speed-Oligo Mycobacteria assay for the identification of NTM. We examined a total of 62 strains (9 type strains, 19 reference strains and 34 clinical isolates) belonging to 13 different species (Mycobacterium intracellulare, M. fortuitum, M. gordonae, M. kansasii, M. marinum, M. peregrinum, M. scrofulaceum, M. abscessus, M. bovis BCG, M. chelonae, M. avium, M. malmoense and M. xenopi). The Speed-Oligo Mycobacteria assay was performed according to the manufacturer's instructions. Discrepant results between Speed-Oligo Mycobacteria and the original identification were reassessed by the Speed-Oligo Mycobacteria assay and resolved by the GenoType Mycobacterium CM assay and by sequencing of 16S rRNA and protein-encoding genes. We found 93.5 % (58/62) concordance for the identification of NTM as compared with the original identification. Three strains were erroneously identified by Speed-Oligo Mycobacteria: one M. kansasii strain was identified as Mycobacterium tuberculosis complex, and one M. chelonae strain and one M. peregrinum strain were both identified as Mycobacterium abscessus. Moreover, one M. chelonae strain was not identified by Speed-Oligo Mycobacteria since it did not react with any species-specific probe. For these strains, sequencing of the genes hsp65, 16S rRNA and rpoB and the GenoType Mycobacterium CM assay were performed. The Speed-Oligo Mycobacteria assay can be a useful tool for the rapid and easy identification of the most common NTM. If applied in clinical practice it could reduce diagnostic delays and contribute to correct clinical and better management of infections caused by NTM.
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Affiliation(s)
- Ivy Bastos Ramis
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium.,Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal de Pelotas, Pelotas, Brazil
| | - Margo Cnockaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Andrea Von Groll
- Laboratório de Micobacteriologia, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Brazil
| | - Vanessa Mathys
- Scientific Institute of Public Health, Brussels, WIV-ISP, Belgium
| | - Anne Simon
- Pôle de Microbiologie, Institut de Recherche Expérimentale et Clinique, UC Louvain, Brussels, Belgium
| | - Enrico Tortoli
- Emerging Bacterial Pathogens Unit, San Raffaele Scientific Institute, Milano, Italy
| | - Juan Carlos Palomino
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Pedro Eduardo Almeida da Silva
- Laboratório de Micobacteriologia, Faculdade de Medicina, Universidade Federal do Rio Grande, Rio Grande, Brazil.,Centro de Desenvolvimento Tecnológico (CDTec), Universidade Federal de Pelotas, Pelotas, Brazil
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Emmanuel Andre
- Pôle de Microbiologie, Institut de Recherche Expérimentale et Clinique, UC Louvain, Brussels, Belgium
| | - Anandi Martin
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
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Muñoz-Dávila MJ, Cejudo García MA, Martínez-Lirola MJ. A comparative evaluation of the sensitivity of one automated and one manual nucleic acid extraction methods for the performance of the Speed-oligo™ Direct Mycobacterium Tuberculosis assay. Enferm Infecc Microbiol Clin 2014; 33:360-1. [PMID: 25444042 DOI: 10.1016/j.eimc.2014.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Revised: 08/01/2014] [Accepted: 09/02/2014] [Indexed: 11/28/2022]
Affiliation(s)
- María José Muñoz-Dávila
- Laboratorio de Microbiología, Unidad de Gestión Clínica de Biotecnología, Complejo Hospitalario Torrecárdenas, 04009 Almería, Spain.
| | - María Aurora Cejudo García
- Laboratorio de Microbiología, Unidad de Gestión Clínica de Biotecnología, Complejo Hospitalario Torrecárdenas, 04009 Almería, Spain
| | - Miguel José Martínez-Lirola
- Laboratorio de Microbiología, Unidad de Gestión Clínica de Biotecnología, Complejo Hospitalario Torrecárdenas, 04009 Almería, Spain
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Hofmann-Thiel S, Hoffmann H. Evaluation of Fluorotype MTB for detection of Mycobacterium tuberculosis complex DNA in clinical specimens from a low-incidence country. BMC Infect Dis 2014; 14:59. [PMID: 24498967 PMCID: PMC3922020 DOI: 10.1186/1471-2334-14-59] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Accepted: 01/30/2014] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND With Fluorotype MTB (FT MTB, HAIN Lifesciences, Germany) a new semi-automated assay for detection of M. tuberculosis complex (MTBC) in clinical specimens has been introduced. In a prospective study, we evaluated the diagnostic performance of FT MTB in a routine diagnostic setting in a low-incidence country. METHODS A total of 1039 respiratory specimens received for routine mycobacteriology diagnostics were analysed by FT MTB. Results were compared to those of culture, microscopy and clinical diagnosis. 61 specimens were excluded from further analysis due to bacterial contamination of cultures. RESULTS FT MTB detected 52 of 59 TB specimens (45 culture-positive with MTBC, 7 with clinical diagnosis of TB). With 902 of 912 non-TB specimens (884 culture-negative, 18 with growth of non-tuberculous mycobacteria) FT MTB was negative; discrepant positive FT MTB results were found with 10 specimens. Overall sensitivity, specificity, positive and negative predictive values were 88.1%, 98.9%, 83.8% and 99.2%. Sensitivity rates for smear-positive and smear-negative TB specimens were 100% and 56.3%, respectively. Seven of 978 samples (0.7%) yielded invalid FT MTB results. CONCLUSIONS FT MTB is a new accurate, half automated assay for rapidly diagnosing TB and suitable for larger series of samples. Performance characteristics were found to be similar to those of other commercial NAATs. Its sensitivity in paucibacillary, smear-negative specimens and its utility for TB diagnostics in high-incidence settings needs to be addressed in further studies.
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Affiliation(s)
- Sabine Hofmann-Thiel
- synlab MVZ Gauting, IML red, WHO Supranational Reference Laboratory of Tuberculosis, Robert-Koch-Allee 2, 82131 Gauting, Germany.
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Malkhed V, Mustyala KK, Potlapally SR, Vuruputuri U. Identification of novel leads applyingin silicostudies for Mycobacterium multidrug resistant (MMR) protein. J Biomol Struct Dyn 2013; 32:1889-906. [DOI: 10.1080/07391102.2013.842185] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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