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Godmer A, Bigey L, Giai-Gianetto Q, Pierrat G, Mohammad N, Mougari F, Piarroux R, Veziris N, Aubry A. Contribution of machine learning for subspecies identification from Mycobacterium abscessus with MALDI-TOF MS in solid and liquid media. Microb Biotechnol 2024; 17:e14545. [PMID: 39257027 PMCID: PMC11387462 DOI: 10.1111/1751-7915.14545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 07/26/2024] [Indexed: 09/12/2024] Open
Abstract
Mycobacterium abscessus (MABS) displays differential subspecies susceptibility to macrolides. Thus, identifying MABS's subspecies (M. abscessus, M. bolletii and M. massiliense) is a clinical necessity for guiding treatment decisions. We aimed to assess the potential of Machine Learning (ML)-based classifiers coupled to Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) MS to identify MABS subspecies. Two spectral databases were created by using 40 confirmed MABS strains. Spectra were obtained by using MALDI-TOF MS from strains cultivated on solid (Columbia Blood Agar, CBA) or liquid (MGIT®) media for 1 to 13 days. Each database was divided into a dataset for ML-based pipeline development and a dataset to assess the performance. An in-house programme was developed to identify discriminant peaks specific to each subspecies. The peak-based approach successfully distinguished M. massiliense from the other subspecies for strains grown on CBA. The ML approach achieved 100% accuracy for subspecies identification on CBA, falling to 77.5% on MGIT®. This study validates the usefulness of ML, in particular the Random Forest algorithm, to discriminate MABS subspecies by MALDI-TOF MS. However, identification in MGIT®, a medium largely used in mycobacteriology laboratories, is not yet reliable and should be a development priority.
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Affiliation(s)
- Alexandre Godmer
- U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), Sorbonne Université, Paris, France
- AP-HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Département de Bactériologie, Groupe Hospitalier Universitaire, Sorbonne Université, Hôpital, Paris, France
| | - Lise Bigey
- U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), Sorbonne Université, Paris, France
- DER (Département d'Enseignement et de Recherche) de Biologie, ENS Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Quentin Giai-Gianetto
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, Paris, France
- Institut Pasteur, Université Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR CNRS 2024, Paris, France
| | - Gautier Pierrat
- AP-HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Département de Bactériologie, Groupe Hospitalier Universitaire, Sorbonne Université, Hôpital, Paris, France
| | - Noshine Mohammad
- Inserm, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, IPLESP, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie- Mycologie, Sorbonne Université, Paris, France
| | - Faiza Mougari
- Service de Mycobactériologie spécialisée et de référence, Centre National de Référence des Mycobactéries (Laboratoire associé), APHP GHU Nord, Université Paris Cité, INSERM IAME UMR, Paris, France
| | - Renaud Piarroux
- Inserm, Institut Pierre-Louis d'Epidémiologie et de Santé Publique, IPLESP, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de Parasitologie- Mycologie, Sorbonne Université, Paris, France
| | - Nicolas Veziris
- U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), Sorbonne Université, Paris, France
- AP-HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Département de Bactériologie, Groupe Hospitalier Universitaire, Sorbonne Université, Hôpital, Paris, France
- AP-HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Alexandra Aubry
- U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi-Paris), Sorbonne Université, Paris, France
- AP-HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
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Zhang H, Tang M, Li D, Xu M, Ao Y, Lin L. Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification. Front Public Health 2024; 12:1410672. [PMID: 38962772 PMCID: PMC11220129 DOI: 10.3389/fpubh.2024.1410672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Non-tuberculous mycobacteria (NTM) infections pose a significant public health challenge worldwide, affecting individuals across a wide spectrum of immune statuses. Recent epidemiological studies indicate rising incidence rates in both immunocompromised and immunocompetent populations, underscoring the need for enhanced diagnostic and therapeutic approaches. NTM infections often present with symptoms similar to those of tuberculosis, yet with less specificity, increasing the risk of misdiagnosis and potentially adverse outcomes for patients. Consequently, rapid and accurate identification of the pathogen is crucial for precise diagnosis and treatment. Traditional detection methods, notably microbiological culture, are hampered by lengthy incubation periods and a limited capacity to differentiate closely related NTM subtypes, thereby delaying diagnosis and the initiation of targeted therapies. Emerging diagnostic technologies offer new possibilities for the swift detection and accurate identification of NTM infections, playing a critical role in early diagnosis and providing more accurate and comprehensive information. This review delineates the current molecular methodologies for NTM species and subspecies identification. We critically assess the limitations and challenges inherent in these technologies for diagnosing NTM and explore potential future directions for their advancement. It aims to provide valuable insights into advancing the application of molecular diagnostic techniques in NTM infection identification.
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Affiliation(s)
- Haiyang Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Maoting Tang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Deyuan Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Min Xu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yusen Ao
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liangkang Lin
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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3
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Abbas M, Khan MT, Iqbal Z, Ali A, Eddine BT, Yousaf N, Wei D. Sources, transmission and hospital-associated outbreaks of nontuberculous mycobacteria: a review. Future Microbiol 2024; 19:715-740. [PMID: 39015998 PMCID: PMC11259073 DOI: 10.2217/fmb-2023-0279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/20/2024] [Indexed: 07/18/2024] Open
Abstract
Nontuberculous mycobacteria (NTM) are widespread environmental organisms found in both natural and man-made settings, such as building plumbing, water distribution networks and hospital water systems. Their ubiquitous presence increases the risk of transmission, leading to a wide range of human infections, particularly in immunocompromised individuals. NTM primarily spreads through environmental exposures, such as inhaling aerosolized particles, ingesting contaminated food and introducing it into wounds. Hospital-associated outbreaks have been linked to contaminated medical devices and water systems. Furthermore, the rising global incidence, prevalence and isolation rates highlight the urgency of addressing NTM infections. Gaining a thorough insight into the sources and epidemiology of NTM infection is crucial for devising novel strategies to prevent and manage NTM transmission and infections.
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Affiliation(s)
- Munawar Abbas
- College of Food Science & Technology, Henan University of Technology, Zhengzhou, Henan, 450001, China
| | - Muhammad Tahir Khan
- Institute of Molecular Biology & Biotechnology (IMBB), The University of Lahore, 1KM Defense Road, Lahore, 58810, Pakistan
- Zhongjing Research & Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan, 473006, PR China
| | - Zafar Iqbal
- School of Life Science, Anhui Normal University, Wuhu, Anhui, China
| | - Arif Ali
- Department of Bioinformatics & Biological Statistics, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Benarfa Taki Eddine
- Echahid Cheikh Larbi Tebessi University Faculty of Exact Sciences & Natural & Life Sciences, Département of Microbiology, Algeria
| | - Numan Yousaf
- Department of Biosciences, COMSATS University Islamabad, Pakistan
| | - Dongqing Wei
- College of Food Science & Technology, Henan University of Technology, Zhengzhou, Henan, 450001, China
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences & School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China
- Zhongjing Research & Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan, 473006, PR China
- Henan Biological Industry Group, 41, Nongye East Rd, Jinshui, Zhengzhou, Henan, 450008, China
- Peng Cheng National Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China
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4
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Opperman CJ, Singh S, Goosen W, Cox H, Warren R, Esmail A. Incorporating direct molecular diagnostics in management algorithms for nontuberculous mycobacteria: Is it high time? IJID REGIONS 2024; 10:140-145. [PMID: 38304760 PMCID: PMC10831244 DOI: 10.1016/j.ijregi.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 02/03/2024]
Abstract
Nontuberculous mycobacteria (NTM) are a group of acid-fast mycobacteria other than Mycobacterium tuberculosis complex (MTBC) that cause pulmonary disease that is similar to the disease caused by MTBC. International guidelines for the diagnosis of pulmonary NTM disease are rigid and have remained unchanged for nearly 2 decades. In this opinion piece, we provide a new perspective on the traditional criteria by suggesting a diagnostic algorithm that incorporates direct molecular identification of NTM performed on raw sputum specimens (using Sanger or targeted deep sequencing approaches, among others) paired with traditional culture methods. Our approach ensures a more rapid diagnosis of pulmonary NTM disease, thus, facilitating timeous clinical diagnosis, and prompt treatment initiation, where indicated, and leverages recent advances in novel molecular techniques into routine NTM identification practice.
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Affiliation(s)
- Christoffel Johannes Opperman
- National Health Laboratory Service, Green Point TB Laboratory, Cape Town, South Africa
- SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Sarishna Singh
- National Health Laboratory Service, Green Point TB Laboratory, Cape Town, South Africa
- SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Wynand Goosen
- SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Helen Cox
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine and Wellcome Centre for Infectious Disease Research, University of Cape Town, Cape Town, South Africa
| | - Rob Warren
- SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Aliasgar Esmail
- UCT Lung Institute, Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town, & Groote Schuur Hospital
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Romagnoli CL, Conceição EC, Machado E, Barreto LBPF, Sharma A, Silva NM, Marques LE, Juliano MA, da Silva Lourenço MC, Digiampietri LA, Suffys PN, Leão SC, Viana-Niero C. Description of new species of Mycobacterium terrae complex isolated from sewage at the São Paulo zoological park foundation in Brazil. Front Microbiol 2024; 15:1335985. [PMID: 38322314 PMCID: PMC10844392 DOI: 10.3389/fmicb.2024.1335985] [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: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 02/08/2024] Open
Abstract
Five mycobacterial isolates from sewage were classified as members of the genus Mycobacterium but presented inconclusive species assignments. Thus, the isolates (MYC017, MYC098, MYC101, MYC123 and MYC340) were analyzed by phenotypical, biochemical, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and genomic features to clarify their taxonomic position. Phenotypic analysis and biochemical tests did not distinguish these isolates from other non-pigmented mycobacteria. In contrast, MALDI-TOF MS analysis showed that isolates were not related to any previously described Mycobacterium species. Comparative genomic analysis showed values of ANI and dDDH between 81.59-85.56% and 24.4-28.8%, respectively, when compared to the genomes of species of this genus. In addition, two (MYC101 and MYC123) presented indistinguishable protein spectra from each other and values of ANI = 98.57% and dDDH = 97.3%, therefore being considered as belonging to the same species. Phylogenetic analysis grouped the five isolates within the Mycobacterium terrae complex (MTC) but in a specific subclade and separated from the species already described and supported by 100% bootstrap value, confirming that they are part of this complex but different from earlier described species. According to these data, we propose the description of four new species belonging to the Mycobacterium genus: (i) Mycobacterium defluvii sp. nov. strain MYC017T (= ATCC TSD-296T = JCM 35364T), (ii) Mycobacterium crassicus sp. nov. strain MYC098T (= ATCC TSD-297T = JCM 35365T), (iii) Mycobacterium zoologicum sp. nov. strain MYC101T (= ATCC TSD-298T = JCM 35366T) and MYC123 (= ATCC BAA-3216 = JCM 35367); and (iv) Mycobacterium nativiensis sp. nov. strain MYC340T (= ATCC TSD-299T = JCM 35368T).
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Affiliation(s)
- Camila Lopes Romagnoli
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Emilyn Costa Conceição
- Laboratório de Bacteriologia e Bioensaios em Micobactérias, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Edson Machado
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Leonardo Bruno Paz Ferreira Barreto
- Laboratório de Bacteriologia e Bioensaios em Micobactérias, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Abhinav Sharma
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Natalia Maria Silva
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Lucas Evangelista Marques
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Maria Cristina da Silva Lourenço
- Laboratório de Bacteriologia e Bioensaios em Micobactérias, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Cristina Viana-Niero
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
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Špičić S, Duvnjak S, Papić B, Reil I, Zrnčić S, Mihaljević Ž, Naletilić Š, Zupičić IG, Kompes G, Habrun B, Mareković I, Zdelar-Tuk M. Description of Mycobacterium pinniadriaticum sp. nov., isolated from a noble pen shell ( Pinna nobilis) population in Croatia. Front Microbiol 2023; 14:1289182. [PMID: 38192290 PMCID: PMC10773828 DOI: 10.3389/fmicb.2023.1289182] [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: 09/05/2023] [Accepted: 11/17/2023] [Indexed: 01/10/2024] Open
Abstract
Introduction Shortly before the mass mortality event of the noble pen shell (Pinna nobilis) population in the south-eastern Adriatic coast, two rapidly growing Mycobacterium strains CVI_P3T (DSM 114013 T, ATCC TSD-295 T) and CVI_P4 were obtained from the organs of individual mollusks during the regular health status monitoring. Methods The strains were identified as members of the genus Mycobacterium using basic phenotypic characteristics, genus-specific PCR assays targeting the hsp65 and 16S rRNA genes and the commercial hybridization kit GenoType Mycobacterium CM (Hain Lifescience, Germany). MALDI-TOF mass spectrometry did not provide reliable identification using the Bruker Biotyper Database. Results and discussion Genome-wide phylogeny and average nucleotide identity (ANI) values confirmed that the studied strains are clearly differentiated from their closest phylogenetic relative Mycobacterium aromaticivorans and other validly published Mycobacterium species (ANI ≤ 85.0%). The type strain CVI_P3T was further characterized by a polyphasic approach using both phenotypic and genotypic methods. Based on the phenotypic, chemotaxonomic and phylogenetic results, we conclude that strains CVI_P3T and CVI_P4 represent a novel species, for which the name Mycobacterium pinniadriaticum sp. nov. is proposed.
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Affiliation(s)
- Silvio Špičić
- Laboratory for Bacterial Zoonosis and Molecular Diagnostics of Bacterial Diseases, Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Sanja Duvnjak
- Laboratory for Bacterial Zoonosis and Molecular Diagnostics of Bacterial Diseases, Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Bojan Papić
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Reil
- Laboratory for Bacterial Zoonosis and Molecular Diagnostics of Bacterial Diseases, Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Snježana Zrnčić
- Laboratory for Fish Pathology, Department for Pathological Morphology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Željko Mihaljević
- Laboratory for Pathology, Department for Pathological Morphology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Šimun Naletilić
- Laboratory for Pathology, Department for Pathological Morphology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Ivana Giovanna Zupičić
- Laboratory for Fish Pathology, Department for Pathological Morphology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Gordan Kompes
- Laboratory for General Bacteriology and Mycology, Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Boris Habrun
- Laboratory for General Bacteriology and Mycology, Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Ivana Mareković
- Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Maja Zdelar-Tuk
- Laboratory for Bacterial Zoonosis and Molecular Diagnostics of Bacterial Diseases, Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
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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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8
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Walczak-Skierska J, Monedeiro F, Maślak E, Złoch M. Lipidomics Characterization of the Microbiome in People with Diabetic Foot Infection Using MALDI-TOF MS. Anal Chem 2023; 95:16251-16262. [PMID: 37877781 PMCID: PMC10633811 DOI: 10.1021/acs.analchem.3c03071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/11/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]
Abstract
Lipidomic profiling has emerged as a powerful tool for the comprehensive characterization of bacterial species, particularly in the context of clinical diagnostics. Utilizing matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), this study aims to elucidate the lipidomic landscapes of bacterial strains isolated from diabetic foot infections (DFI). Our analysis successfully identified a diverse array of lipids in the cellular membranes of both Gram-positive and Gram-negative bacteria, revealing a total of 108 unique fatty acid combinations. Specifically, we identified 26 LPG, 33 LPE, 43 PE, 114 PG, 89 TAG, and 120 CLP in Gram-positive bacteria and 10 LPG, 14 LPE, 124 PE, 37 PG, 13 TAG, and 22 CLP in Gram-negative strains. Key fatty acids, such as palmitic acid, palmitoleic acid, stearic acid, and oleic acid, were prominently featured. Univariate analysis further highlighted distinct lipidomic signatures among the bacterial strains, revealing elevated levels of phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) in Gram-negative bacteria associated with DFI. In contrast, Gram-positive strains demonstrated increased or uniquely fluctuating levels of triglyceride (TAG) and cardiolipin (CLP). These findings not only underscore the utility of MALDI-TOF MS in bacterial lipidomics but also provide valuable insights into the lipidomic adaptations of bacteria in diabetic foot infections, thereby laying the groundwork for future studies aimed at constructing microbial lipid libraries for enhanced bacterial identification.
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Affiliation(s)
- Justyna Walczak-Skierska
- Centre
for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland
- Chair
of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus a Copernicus University in Toruń, Gagarina 7 Str., 87-100 Toruń, Poland
| | - Fernanda Monedeiro
- Centre
for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland
| | - Ewelina Maślak
- Centre
for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland
| | - Michał Złoch
- Centre
for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland
- Chair
of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus a Copernicus University in Toruń, Gagarina 7 Str., 87-100 Toruń, Poland
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9
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Manbenmad V, So-Ngern A, Chetchotisakd P, Faksri K, Ato M, Nithichanon A, Lertmemongkolchai G. Evaluating anti-GPL-core IgA as a diagnostic tool for non-tuberculous mycobacterial infections in Thai patients with high antibody background. Sci Rep 2023; 13:18883. [PMID: 37919326 PMCID: PMC10622420 DOI: 10.1038/s41598-023-45893-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023] Open
Abstract
Diagnosis of non-tuberculous mycobacterial (NTM) infection is difficult due to low sensitivity and time-consuming laboratory tests. Current serological assays fail in tropical countries due to high antibody background. This study aimed to investigate an appropriate method for detecting anti-glycopeptidolipid (GPL)-core antibodies to diagnose NTM infection in Thailand. Heparinized plasma samples were collected from 20 patients with NTM-pulmonary disease (NTM-PD) and 22 patients with disseminated NTM (dNTM) for antibody detection by ELISA. The results were compared with those from patients with tuberculosis, other bacterial pulmonary infections and healthy controls. Among the different antibody isotypes, anti-GPL-core IgA exhibited the highest suitability. Therefore, anti-GPL-core IgA and its subclass IgA2 were further investigated. A significant increase in antibody levels was observed during the active infection stage, whereas NTM-PD with culture conversion at the 6-month follow-up showed reduced IgA levels. The diagnostic cut-off for IgA and IgA2 was newly defined as 1.4 and 1.0 U/ml, respectively. Using our IgA cut-off, the sensitivity and specificity for diagnosing NTM-PD were 77.3% and 81.4%, respectively. The new IgA cut-off demonstrated significantly improved specificity compared to the manufacturer's cut-off. Thus, serological detection of anti-GPL-core IgA, with a cut-off of 1.4 U/ml, can be a valuable tool for supporting NTM diagnosis in Thailand.
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Affiliation(s)
- Varis Manbenmad
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Apichart So-Ngern
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | | | - Kiatichai Faksri
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Manabu Ato
- Department of Mycobacteriology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Arnone Nithichanon
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
| | - Ganjana Lertmemongkolchai
- Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand.
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10
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Curtoni A, Cordovana M, Bondi A, Scaiola F, Criscione G, Ghibaudo D, Pastrone L, Zanotto E, Camaggi A, Caroppo MS, Kostrzewa M, Cavallo R, Costa C. Application of FT-IR Spectroscopy for Mycobacterium abscessus complex subspecies differentiation. J Microbiol Methods 2023; 212:106792. [PMID: 37517511 DOI: 10.1016/j.mimet.2023.106792] [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: 06/12/2023] [Revised: 07/27/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
Mycobacterium abscessus complex (MABSC) subspecies differentiation improves patients' therapy and outcome. Fourier-Transform-Infrared Spectroscopy (FT-IRS) was applied for subspecies discrimination of 15 strains on different media: Löwenstein-Jensen showed the best resolution power; Linear Discriminant Analysis model differentiated M. abscessus susbsp. abscessus from M. abscessus subsp. massiliense. FT-IRS has a potential role in rapidly MABSC subspecies identification.
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Affiliation(s)
- Antonio Curtoni
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy; Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | | | - Alessandro Bondi
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy; Department of Public Health and Paediatrics, University of Turin, Turin, Italy.
| | - Francesca Scaiola
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Giulia Criscione
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Davide Ghibaudo
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Lisa Pastrone
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Elisa Zanotto
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy
| | - Anna Camaggi
- Microbiology and Virology Unit, Azienda Ospedaliero-Universitaria Maggiore della Carità di Novara, Novara, Italy
| | - Maria Simona Caroppo
- Microbiology and Virology Unit, Azienda Ospedaliero-Universitaria Maggiore della Carità di Novara, Novara, Italy
| | - Markus Kostrzewa
- Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Rossana Cavallo
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy; Department of Public Health and Paediatrics, University of Turin, Turin, Italy
| | - Cristina Costa
- Microbiology and Virology Unit, University Hospital Città della Salute e della Scienza di Torino, Turin, Italy; Department of Public Health and Paediatrics, University of Turin, Turin, Italy
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11
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Faury HB, Awad Z, Jolivet S, Le Neindre K, Couturier J, Godmer A, Colle R, Levi LI, Cambau E, Barbut F. Investigation of a Mycobacterium fortuitum catheter-related bloodstream infection in an oncology unit. Infect Control Hosp Epidemiol 2023; 44:1342-1344. [PMID: 36804097 DOI: 10.1017/ice.2022.263] [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: 02/22/2023]
Abstract
We describe a case of healthcare-associated bloodstream infection due to Mycobacterium fortuitum. Whole-genome sequencing showed that the same strain was isolated from the shared shower water of the unit. Nontuberculous mycobacteria frequently contaminate hospital water networks. Preventative actions are needed to reduce the exposure risk for immunocompromised patients.
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Affiliation(s)
- Hélène B Faury
- Unité de Prévention du Risque Infectieux, Assistance Publique-Hôpitaux de Paris, GHU, Sorbonne Université, Hôpital Saint-Antoine, Paris, France
| | - Zeina Awad
- Service de Mycobactériologie Spécialisée et de Référence, Laboratoire Associé du Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Assistance Publique-Hôpitaux de Paris, GHU Nord, Hôpital Bichat, Paris, France
| | - Sarah Jolivet
- Unité de Prévention du Risque Infectieux, Assistance Publique-Hôpitaux de Paris, GHU, Sorbonne Université, Hôpital Saint-Antoine, Paris, France
| | - Killian Le Neindre
- Laboratoire de Microbiologie de l'Environnement, Assistance Publique-Hôpitaux de Paris, GHU, Sorbonne Université, Hôpital Saint-Antoine, Paris, France
- Université Paris Cité, INSERM S-1139, 3PHM, France
| | - Jeanne Couturier
- Laboratoire de Microbiologie de l'Environnement, Assistance Publique-Hôpitaux de Paris, GHU, Sorbonne Université, Hôpital Saint-Antoine, Paris, France
- Université Paris Cité, INSERM S-1139, 3PHM, France
| | - Alexandre Godmer
- Département de Microbiologie, Assistance Publique-Hôpitaux de Paris, GHU, Sorbonne Université, Hôpital Saint-Antoine, Paris, France
| | - Raphaël Colle
- Département d'Oncologie Médicale, Assistance Publique-Hôpitaux de Paris, GHU, Sorbonne Université, Hôpital Saint-Antoine, Paris, France
| | - Laura I Levi
- Service des Maladies Infectieuses et Tropicales, Assistance Publique-Hôpitaux de Paris, GHU, Sorbonne Université, Hôpital Saint-Antoine, Paris, France
| | - Emmanuelle Cambau
- Service de Mycobactériologie Spécialisée et de Référence, Laboratoire Associé du Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Assistance Publique-Hôpitaux de Paris, GHU Nord, Hôpital Bichat, Paris, France
- Université Paris Cité, INSERM UMR1137 IAME, Paris, France
| | - Frédéric Barbut
- Unité de Prévention du Risque Infectieux, Assistance Publique-Hôpitaux de Paris, GHU, Sorbonne Université, Hôpital Saint-Antoine, Paris, France
- Laboratoire de Microbiologie de l'Environnement, Assistance Publique-Hôpitaux de Paris, GHU, Sorbonne Université, Hôpital Saint-Antoine, Paris, France
- Université Paris Cité, INSERM S-1139, 3PHM, France
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12
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Shi J, Gao G, Pan J, Wu LP, Ning H, Wu Z, Ye X, Jiang X. Strain Identification and Drug Resistance Analysis of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry in Nontuberculous Mycobacterial Lung Disease. Infect Drug Resist 2023; 16:4635-4643. [PMID: 37484902 PMCID: PMC10361085 DOI: 10.2147/idr.s405563] [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: 01/20/2023] [Accepted: 04/14/2023] [Indexed: 07/25/2023] Open
Abstract
Objective To evaluate the clinical value of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in detecting Nontuberculous mycobacteria (NTM). Methods The clinical data of 172 patients with suspected NTM lung disease were collected from our hospital from January 1, 2018, to December 30, 2021. The results were compared with those of BACTEC MGIT 960 in liquid culture and gene chip. This study also utilised MALDI-TOF MS to detect macrolide (MA) and amikacin (Am) mutations. Results One hundred thirty-seven cases of NTM pulmonary disease were confirmed by identifying the NTM gene chip in bronchoalveolar lavage fluid and/or MALDI-TOF MS detection. The positive predictive value and negative predictive value were 100% (131/131) and 85.37% (35/41), respectively, and the consistency of the two methods was high (kappa=0.899). For the drug resistance detection of MAs, the consistency rate between MALDI-TOF MS detection and drug sensitivity detection was 97.71% (128/131), the sensitivity was 81.25% (13/16) and the specificity was 100% (115/115). The positive and negative predictive values were 100% (13/13) and 93.75% (115/118), respectively. There was no coincidental consistency between the two methods, and the consistency was high (P<0.001, kappa=0.884). For the drug resistance test of Am, the consistency rate between the MALDI-TOF MS test and the drug sensitivity test was 93.13% (122/131), the sensitivity was 93.52% (101/108), the specificity was 90.91% (21/23) and the positive predictive value and negative predictive value were 98.06% (101/103) and 75.00% (21/28), respectively. The two methods had high consistency, and the consistency was not coincidental (P<0.001, kappa=0.781). Conclusion Utilising MALDI-TOF MS has a good consistency with the drug resistance gene chip method and can be a rapid and effective method to identify strains and drug resistance of NTM. Therefore, it has certain clinical application value in patients with suspected NTM lung disease.
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Affiliation(s)
- Jichan Shi
- Department of Infectious Disease, The Theorem Clinical College of Wenzhou Medical University, Wenzhou Central Hospital, Wenzhou, People’s Republic of China
| | - Gexin Gao
- Department of Nursing, Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - Jing Pan
- Department of Geriatric Medicine, The Theorem Clinical College of Wenzhou Medical University, Wenzhou Central Hospital, Wenzhou, People’s Republic of China
| | - Lian-Peng Wu
- Department of Laboratory, The Dingli Clinical Institute of Wenzhou Medical University, Wenzhou Central Hospital, Wenzhou, People’s Republic of China
| | - Hongye Ning
- Department of Infectious Disease, The Theorem Clinical College of Wenzhou Medical University, Wenzhou Central Hospital, Wenzhou, People’s Republic of China
| | - Zhengxin Wu
- Department of Infectious Disease, The Theorem Clinical College of Wenzhou Medical University, Wenzhou Central Hospital, Wenzhou, People’s Republic of China
| | - Xinchun Ye
- Department of Infectious Disease, The Theorem Clinical College of Wenzhou Medical University, Wenzhou Central Hospital, Wenzhou, People’s Republic of China
| | - Xiangao Jiang
- Department of Infectious Disease, The Theorem Clinical College of Wenzhou Medical University, Wenzhou Central Hospital, Wenzhou, People’s Republic of China
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13
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Tsiolakkis G, Liontos A, Filippas-Ntekouan S, Matzaras R, Theodorou E, Vardas M, Vairaktari G, Nikopoulou A, Christaki E. Mycobacterium marinum: A Case-Based Narrative Review of Diagnosis and Management. Microorganisms 2023; 11:1799. [PMID: 37512971 PMCID: PMC10384600 DOI: 10.3390/microorganisms11071799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Skin and soft tissue infections caused by non-tuberculous mycobacteria are occurring more frequently in recent years. However, chronic skin and soft tissue lesions present a challenge for clinicians, as the diagnostic work-up and definitive diagnosis require knowledge and available laboratory resources. We present here the case of a 66-year-old male patient who presented with painful abscess-like nodules on his right hand and forearm, which worsened after treatment with an anti-TNF-a agent. The fluid specimen taken from the lesion was positive for mycobacteria according to the acid-fast stain. Mycobacterium marinum was identified, first by next-generation sequencing and finally grown on culture, after eight weeks. Acknowledging the complexity of diagnosing and managing infections by non-tuberculous mycobacteria, and especially Mycobacterium marinum, we provide a review of the current epidemiology, clinical characteristics, diagnosis and management of Mycobacterium marinum infection.
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Affiliation(s)
- Giorgos Tsiolakkis
- Department of Internal Medicine, Nicosia General Hospital, Nicosia 2029, Cyprus
| | - Angelos Liontos
- 1st Division of Internal Medicine & Infectious Diseases Unit, University General Hospital of Ioannina, Faculty of Medicine, University of Ioannina, Str. Niarchou, 45500 Ioannina, Greece
| | - Sempastian Filippas-Ntekouan
- 1st Division of Internal Medicine & Infectious Diseases Unit, University General Hospital of Ioannina, Faculty of Medicine, University of Ioannina, Str. Niarchou, 45500 Ioannina, Greece
| | - Rafail Matzaras
- 1st Division of Internal Medicine & Infectious Diseases Unit, University General Hospital of Ioannina, Faculty of Medicine, University of Ioannina, Str. Niarchou, 45500 Ioannina, Greece
| | | | - Michail Vardas
- School of Medicine, University of Cyprus, Nicosia 2029, Cyprus
| | | | - Anna Nikopoulou
- Department of Internal Medicine, G. Papanikolaou General Hospital of Thessaloniki, 57010 Thessaloniki, Greece
| | - Eirini Christaki
- 1st Division of Internal Medicine & Infectious Diseases Unit, University General Hospital of Ioannina, Faculty of Medicine, University of Ioannina, Str. Niarchou, 45500 Ioannina, Greece
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14
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Hershko Y, Adler A. Antimicrobial Susceptibility Distributions of Clinical Isolates of Nontuberculous Mycobacteria in Israel. Microb Drug Resist 2023. [PMID: 37219996 DOI: 10.1089/mdr.2023.0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
There is a scarcity of data regarding the antimicrobial susceptibility testing profiles of nontuberculous mycobacterial (NTM) in Israel and other Middle Eastern countries. We aimed to describe the antimicrobial susceptibility profiles of NTM in Israel. A total of 410 clinical isolates of NTM, identified to the species level using matrix-assisted laser desorption ionization-time of flight mass spectrometry or hsp65 gene sequencing, were included. Minimum inhibitory concentrations for slowly growing mycobacteria (SGM) and rapidly growing mycobacteria (RGM) for 12 and 11 drugs were determined using the Sensititre SLOMYCOI and RAPMYCOI broth microdilution plates, respectively. Mycobacterium avium complex (MAC) was the most frequently isolated species (n = 148; 36%), followed by Mycobacterium simiae (n = 93; 23%), Mycobacterium abscessus group (n = 62; 15%), Mycobacterium kansasii (n = 27; 7%), and Mycobacterium fortuitum (n = 22; 5%) accounting together for 86% of isolates. The most active agents against SGM were amikacin (98%/85%/100%) and clarithromycin (97%/99%/100%), followed by moxifloxacin (25%/10%/100%) and linezolid (3%/6%/100%) for MAC, M. simiae, and M. kansasii, respectively. For RGM, the most active agents were amikacin (98%/100%/88%) followed by linezolid (48%/80%/100%) and clarithromycin (39%/28%/94%) for M. abscessus group, M. fortuitum, and M. chelonae, respectively. These findings can assist in guiding the treatment of NTM infections.
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Affiliation(s)
- Yizhak Hershko
- Clinical Microbiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv University, Tel-Aviv, Israel
| | - Amos Adler
- Clinical Microbiology Laboratory, Tel-Aviv Sourasky Medical Center, Tel-Aviv University, Tel-Aviv, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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15
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Maślak E, Arendowski A, Złoch M, Walczak-Skierska J, Radtke A, Piszczek P, Pomastowski P. Silver Nanoparticle Targets Fabricated Using Chemical Vapor Deposition Method for Differentiation of Bacteria Based on Lipidomic Profiles in Laser Desorption/Ionization Mass Spectrometry. Antibiotics (Basel) 2023; 12:antibiotics12050874. [PMID: 37237776 DOI: 10.3390/antibiotics12050874] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/05/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
The global threat of numerous infectious diseases creates a great need to develop new diagnostic methods to facilitate the appropriate prescription of antimicrobial therapy. More recently, the possibility of using bacterial lipidome analysis via laser desorption/ionization mass spectrometry (LDI-MS) as useful diagnostic tool for microbial identification and rapid drug susceptibility has received particular attention because lipids are present in large quantities and can be easily extracted similar to ribosomal proteins. Therefore, the main goal of the study was to evaluate the efficacy of two different LDI techniques-matrix-assisted (MALDI) and surface-assisted (SALDI) approaches-in the classification of the closely related Escherichia coli strains under cefotaxime addition. Bacterial lipids profiles obtained by using the MALDI technique with different matrices as well as silver nanoparticle (AgNP) targets fabricated using the chemical vapor deposition method (CVD) of different AgNP sizes were analyzed by the means of different multivariate statistical methods such as principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), sparse partial least squares discriminant analysis (sPLS-DA), and orthogonal projections to latent structures discriminant analysis (OPLS-DA). The analysis showed that the MALDI classification of strains was hampered by interference from matrix-derived ions. In contrast, the lipid profiles generated by the SALDI technique had lower background noise and more signals associated with the sample, allowing E. coli to be successfully classified into cefotaxime-resistant and cefotaxime-sensitive strains, regardless of the size of the AgNPs. AgNP substrates obtained using the CVD method were used for the first time for distinguishing closely related bacterial strains based on their lipidomic profiles and demonstrate high potential as a future diagnostic tool for the detection of antibiotic susceptibility.
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Affiliation(s)
- Ewelina Maślak
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland
| | - Adrian Arendowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland
| | - Michał Złoch
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland
- Chair of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7 Str., 87-100 Toruń, Poland
| | - Justyna Walczak-Skierska
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland
| | - Aleksandra Radtke
- Department of Inorganic and Coordination Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7 Str., 87-100 Toruń, Poland
- Nano-Implant Ltd., Gagarina 5/102, 87-100 Toruń, Poland
| | - Piotr Piszczek
- Department of Inorganic and Coordination Chemistry, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7 Str., 87-100 Toruń, Poland
- Nano-Implant Ltd., Gagarina 5/102, 87-100 Toruń, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Wileńska 4 Str., 87-100 Toruń, Poland
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16
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Broncano-Lavado A, Barrado L, Lopez-Roa P, Cacho J, Domingo D, Hernandez S, Garcia-Martinez J, Millan MR, Perez-Cecilia E, Ruiz-Serrano MJ, Salso S, Simon M, Tato M, Toro C, Valverde-Canovas JF, Esteban J. Clinical Evaluation of Nontuberculous Mycobacteria (NTM) Elite Agar, a New Medium for the Isolation of NTM: a Multicenter Study. J Clin Microbiol 2023; 61:e0003623. [PMID: 36975783 PMCID: PMC10117115 DOI: 10.1128/jcm.00036-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/04/2023] [Indexed: 03/29/2023] Open
Abstract
Nontuberculous mycobacteria (NTM) are gaining interest with the increased number of infected patients. NTM Elite agar is designed specifically for the isolation of NTM without the decontamination step. We assessed the clinical performance of this medium combined with Vitek mass spectrometry (MS) matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) technology for the isolation and identification of NTM in a prospective multicenter study, including 15 laboratories (24 hospitals). A total of 2,567 samples from patients with suspected NTM infection were analyzed (1,782 sputa, 434 bronchial aspirates, 200 bronchoalveolar lavage samples, 34 bronchial lavage samples, and 117 other samples). A total of 220 samples (8.6%) were positive with existing laboratory methods against 330 with NTM Elite agar (12.8%). Using the combination of both methods, 437 isolates of NTM were detected in 400 positive samples (15.6% of samples). In total, 140 samples of the standard procedures (SP) and 98 of the NTM Elite agar were contaminated. NTM Elite agar showed a higher performance for rapidly growing mycobacteria (RGM) species than SP (7% versus 3%, P < 0.001). A trend has been noted for the Mycobacterium avium complex (4% with SP versus 3% with NTM Elite agar, P = 0.06). The time to positivity was similar (P = 0.13) between groups. However, the time to positivity was significantly shorter for the RGM in subgroup analysis (7 days with NTM and 6 days with SP, P = 0.01). NTM Elite agar has been shown to be useful for the recovery of NTM species, especially for the RGM. Using NTM Elite agar + Vitek MS system in combination with SP increases the number of NTM isolated from clinical samples.
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Affiliation(s)
| | - Laura Barrado
- Department of Clinical Microbiology, Hospital Universitario de Móstoles, Móstoles, Madrid, Spain
| | - Paula Lopez-Roa
- Department of Microbiology, Hospital Universitario, Madrid, Spain
| | - Juana Cacho
- Department of Microbiology, Hospital Universitario de Getafe, Getafe, Madrid, Spain
| | - Diego Domingo
- Department of Microbiology, Hospital Universitario de La Princesa, Madrid, Spain
| | - Sara Hernandez
- Microbiology Laboratory, Hospital Severo Ochoa, Leganés, Madrid, Spain
| | | | - Maria Rosario Millan
- Department of Microbiology, H.U. Puerta de Hierro-Majadahonda, Majadahonda, Madrid, Spain
| | | | - Maria-Jesus Ruiz-Serrano
- Department of Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- CIBERES-CIBER de Enfermedades Respiratorias, Madrid, Spain
| | - Santiago Salso
- Clinical Laboratory, UR Salud. Paseo de Europa, San Sebastián de los Reyes, Madrid, Spain
| | - Maria Simon
- Department of Microbiology and Parasitology, Hospital Central de la Defensa Gomez Ulla, Madrid, Spain
| | - Marta Tato
- Department of Microbiology, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | - Carlos Toro
- Department of Microbiology, Hospital Universitario La Paz, Madrid, Spain
| | | | - Jaime Esteban
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, Madrid, Spain
- CIBERINFEC-CIBER de Enfermedades Infecciosas, Madrid, Spain
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17
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Markanović M, Makek MJ, Glodić G, Kuliš T, Mareković I. Evaluation and clinical impact of MALDI Biotyper Mycobacteria Library v6.0 for identification of nontuberculous mycobacteria by MALDI-TOF mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4915. [PMID: 37010443 DOI: 10.1002/jms.4915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/03/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Major challenges in the identification of non-tuberculous mycobacteria (NTM) by MALDI-TOF MS include protein extraction protocol and updating of the NTM database. The aim of this study was to evaluate MALDI Biotyper Mycobacteria Library v6.0 (Bruker Daltonics GmbH, Bremen, Germany) for identification of clinical NTM isolates and its impact on clinical management. NTM isolates cultivated from clinical samples in 101 patients were identified simultaneously by PCR-reverse hybridization (Hain Lifescience GmbH, Nehren, Germany) as a routinely used reference molecular method and using MALDI Biotyper Microflex LT/SH after protein extraction. Each isolate was applied to eight spots, and mean scores were used in analysis. MALDI-TOF MS obtained correct identification to the species level for 95 (94.06%) NTM isolates. The majority of correctly identified isolates (92/95; 96.84%) were identified with high-confidence score of ≥1.80 and only 3.16% (3/95) with a score of <1.80. Mean value ± SD of RGM NTM isolates (2.127 ± 0.172) was statistically significant higher in comparison to SGM NTM isolates (2.027 ± 0.142) with a p value of 0.007. In comparison to PCR-reverse hybridization, discordant identification results by MALDI-TOF MS were found in six (6/101; 5.94%) NTM isolates for which clinical data were analyzed. We demonstrated a high confidence NTM identifications using Mycobacterium Library v 6.0 on routine clinical isolates. This is the first study that analyzed MALDI-TOF MS identification results of NTM isolates in the context of clinical data, and it showed that MALDI-TOF MS with its updated databases could help clarify the epidemiology, clinical characteristics, and course of infections caused by less frequent NTM species.
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Affiliation(s)
- Manda Markanović
- Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, Zagreb, 10 000, Croatia
| | - Mateja Janković Makek
- School of Medicine, University of Zagreb, Zagreb, 10 000, Croatia
- Department of Respiratory Diseases, University Hospital Centre Zagreb, Zagreb, 10 000, Croatia
| | - Goran Glodić
- Department of Respiratory Diseases, University Hospital Centre Zagreb, Zagreb, 10 000, Croatia
| | - Tomislav Kuliš
- Department of Urology, University Hospital Centre Zagreb, Zagreb, 10 000, Croatia
| | - Ivana Mareković
- Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, Zagreb, 10 000, Croatia
- School of Medicine, University of Zagreb, Zagreb, 10 000, Croatia
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18
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Fukushima K, Matsumoto Y, Matsuki T, Saito H, Motooka D, Komukai S, Fukui E, Yamuchi J, Nitta T, Niitsu T, Abe Y, Nabeshima H, Nagahama Y, Nii T, Tsujino K, Miki K, Kitada S, Kumanogoh A, Akira S, Nakamura S, Kida H. MGIT-seq for the Identification of Nontuberculous Mycobacteria and Drug Resistance: a Prospective Study. J Clin Microbiol 2023; 61:e0162622. [PMID: 36946719 PMCID: PMC10117113 DOI: 10.1128/jcm.01626-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Because nontuberculous mycobacterial pulmonary disease is a considerable health burden, a simple and clinically applicable analytical protocol enabling the identification of subspecies and drug-resistant disease is required to determine the treatment strategy. We aimed to develop a simplified workflow consisting only of direct sequencing of mycobacterial growth indicator tube cultures (MGIT-seq). In total, 138 patients were prospectively enrolled between April 2021 and May 2022, and culture-positive MGIT broths were subjected to sequencing using MinION, a portable next-generation sequencer. Sequence analysis was conducted to identify species using core genome multilocus sequence typing and to predict macrolide and amikacin (AMK) resistance based on previously reported mutations in rrl, rrs, and erm(41). The results were compared to clinical tests for species identification and drug susceptibility. A total of 116 patients with positive MGIT cultures were included in the analysis. MGIT-seq yielded 99.1% accuracy in species-level identification and identified 98 isolates (84.5%) at the subspecies level. Macrolide and AMK resistance were detected in 19.4% and 1.9% of Mycobacterium avium complex (MAC) and Mycobacterium abscessus isolates. The predicted macrolide and AMK resistance was consistent with the results of conventional drug susceptibility tests, with specificities of 97.6% and 100.0%, respectively. Direct MGIT-seq has achieved comprehensive identification and drug resistance detection of nontuberculous mycobacteria, which could be applicable to determine the treatment strategy by a single test in clinical practice.
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Affiliation(s)
- Kiyoharu Fukushima
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
- Global Center for Medical Engineering and Informatics, Suita, Osaka, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Takanori Matsuki
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Haruko Saito
- Department of Clinical Laboratory, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Sho Komukai
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
- Department of Biomedical Statistics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Eriko Fukui
- Department of General Thoracic surgery, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - June Yamuchi
- Department of Clinical Laboratory, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan
| | - Tadayoshi Nitta
- Department of Clinical Laboratory, National Hospital Organization, Osaka Toneyama Medical Centre, Toyonaka, Osaka, Japan
| | - Takayuki Niitsu
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuko Abe
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Hiroshi Nabeshima
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Yasuharu Nagahama
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Takuro Nii
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Kazuyuki Tsujino
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Keisuke Miki
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | | | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Japan for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka, Japan
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Japan for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Hiroshi Kida
- Department of Respiratory Medicine, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
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Xiong L, Long X, Ni L, Wang L, Zhang Y, Cui L, Guo J, Yang C. Comparison of Autof Ms1000 and EXS3000 MALDI-TOF MS Platforms for Routine Identification of Microorganisms. Infect Drug Resist 2023; 16:913-921. [PMID: 36814830 PMCID: PMC9939805 DOI: 10.2147/idr.s352307] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 12/20/2022] [Indexed: 02/16/2023] Open
Abstract
Purpose Matrix-assisted laser desorption-ionization-time of flight mass spectrometry (MALDI-TOF) has recently been widely used in clinical microbiology laboratories, with the advantages of being reliable, rapid, and cost-effective. Here, we reported the performance of two MALDI-TOF MS instruments, EXS3000 (Zybio, China) and Autof ms1000 (Autobio, China), which are commonly used in clinical microbiology field. Methods A total of 209 common clinical common isolates, including 70 gram-negative bacteria strains, 58 gram-positive bacteria strains, 33 yeast strains, 15 anaerobic bacteria strains, and 33 mold strains, and 19 mycobacterial strains were tested. All strains were identified by EXS3000 (Zybio, China) and Autof ms1000 (Autobio, China). Sequence analysis of 16S rRNA or ITS regions was used to verify all strains. Results Current study found that species-level discrimination was found to be 191 (91.39%) and 190 (90.91%) by EXS3000 and Autof ms1000, respectively. Genus-level discrimination was 205 (98.09%) by the EXS3000 and 205 (98.09%) by the Autof ms1000, respectively. The correct results at species level of the EXS3000 were 91.43% (64/70) for gram-negative bacteria, 93.1% (54/58) for gram-positive cocci, 93.94% (31/33) for yeast, 100% (15/15) for anaerobes and 81.82% (27/33) for filamentous fungi. The correct results at species level of the Autof ms1000 were 92.86% (65/70) for gram-negative bacteria, 91.38% (53/58) for gram-positive cocci, 93.94% (31/33) for yeast, 100% (15/15) for anaerobes and 78.79% (26/33) for filamentous fungi. Conclusion Although the results show that the EXS3000 and Autof ms1000 systems are equally good choices in terms of analytical efficiency for routine procedures, the test result of EXS3000 is slightly better than Autof ms1000. It's worth mentioning that the target plate of the EXS 3000 instrument is reusable, but the target plate of the Autof ms1000 is disposable, making the EXS3000 more effective in reducing costs.
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Affiliation(s)
- Lijuan Xiong
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guizhou, People’s Republic of China
| | - Xu Long
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guizhou, People’s Republic of China
| | - Lijun Ni
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Lili Wang
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China
| | - Yang Zhang
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guizhou, People’s Republic of China
| | - Lili Cui
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guizhou, People’s Republic of China
| | - Jian Guo
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, People’s Republic of China,Correspondence: Jian Guo, Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, No. 1800 Yuntai Road, Pudong New Area, Shanghai, People’s Republic of China, Tel +86-17701810639, Email
| | - Chunying Yang
- Department of Laboratory Medicine, the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guizhou, People’s Republic of China,Chunying Yang, Department of Laboratory Medicine, the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, No. 83 Feishan Street, Yunyan District, Guiyang City, Guizhou Province, People’s Republic of China, Tel +86-13658504875, Email
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20
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Identification of Mycobacterium abscessus Subspecies by MALDI-TOF Mass Spectrometry and Machine Learning. J Clin Microbiol 2023; 61:e0111022. [PMID: 36602341 PMCID: PMC9879094 DOI: 10.1128/jcm.01110-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium abscessus is one of the most common and pathogenic nontuberculous mycobacteria (NTM) isolated in clinical laboratories. It consists of three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense. Due to their different antibiotic susceptibility pattern, a rapid and accurate identification method is necessary for their differentiation. Although matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has proven useful for NTM identification, the differentiation of M. abscessus subspecies is challenging. In this study, a collection of 325 clinical isolates of M. abscessus was used for MALDI-TOF MS analysis and for the development of machine learning predictive models based on MALDI-TOF MS protein spectra. Overall, using a random forest model with several confidence criteria (samples by triplicate and similarity values >60%), a total of 96.5% of isolates were correctly identified at the subspecies level. Moreover, an improved model with Spanish isolates was able to identify 88.9% of strains collected in other countries. In addition, differences in culture media, colony morphology, and geographic origin of the strains were evaluated, showing that the latter had an impact on the protein spectra. Finally, after studying all protein peaks previously reported for this species, two novel peaks with potential for subspecies differentiation were found. Therefore, machine learning methodology has proven to be a promising approach for rapid and accurate identification of subspecies of M. abscessus using MALDI-TOF MS.
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21
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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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22
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Maheshwari S, Parakh S, Das SM, Ahuja A, Jha SN, Agrawal R, Gupta V, Luthra S. Multifocal Serpiginoid Choroiditis Due to Mycobacterium Mageritense following Laparoscopic Hysterectomy in an Immunocompetent Host. Ocul Immunol Inflamm 2023; 31:236-241. [PMID: 35050821 DOI: 10.1080/09273948.2021.2018713] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
PURPOSE To report nontubercular choroiditis, caused by Mycobacterium mageritense isolated using MALDI-TOF MS, following laparoscopic hysterectomy in an immunocompetent patient. CASE REPORT A 42-year-old female presented with gradual, painless diminution of vision in the right eye for six weeks. She had undergone laparoscopic hysterectomy two months back. BCVA was 2/60 OD. Clinical presentation and imaging all pointed to a diagnosis of serpiginous-like choroiditis. Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) had led to isolation of Mycobacterium mageritense. Patient was treated with systemic antibiotics. At 3 months follow up, BCVA improved to 6/60; fundus showed healed choroiditis and chorioretinal thinning. CONCLUSION Atypical mycobacterial infections associated with laparoscopic surgeries can rarely lead to debilitating systemic bacteremia resulting in profound visual impairment. The importance of timely diagnosis using specific and sophisticated methods such as MALDI-TOF MS as well as maintaining aseptic precautions perioperatively during major surgeries cannot be overemphasized.
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Affiliation(s)
| | - Shweta Parakh
- Drishti Eye Institute, Drishti Eye Institute, Dehradun, India
| | | | - Alok Ahuja
- Dr. Ahuja's Pathology and Imaging Centre, Dr. Ahuja's Pathology and Imaging Centre, Dehradun, India
| | - Shashi Nath Jha
- Sir Ganga Ram Hospital, Sir Ganga Ram Hospital, New Delhi, India
| | - Rupesh Agrawal
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Vishali Gupta
- Advanced Eye Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Saurabh Luthra
- Drishti Eye Institute, Drishti Eye Institute, Dehradun, India
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Using Vitek MS v3.0 To Identify Nontuberculous Mycobacteria in Liquid Media in a Clinical Microbiology Laboratory. Microbiol Spectr 2022; 10:e0201822. [PMID: 36287015 PMCID: PMC9769768 DOI: 10.1128/spectrum.02018-22] [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] [Indexed: 01/06/2023] Open
Abstract
Recently, the incidence of diseases caused by nontuberculous mycobacteria (NTM) has been increasing worldwide, especially in immunocompromised patients and those with potential chronic lung disease. Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and reliable method for identifying mycobacteria in clinical laboratories. This study aimed to evaluate the performance of Vitek MS v3.0 by isolating NTM directly from automated liquid medium systems using patient samples. A total of 855 Mycobacterium growth indicator tube (MGIT)-positive liquid cultures were investigated. Among them, 658 (77.0%) liquid cultures were correctly identified to the species, group, or complex level, 192 (23.0%) resulted in no identification, and 5 (0.6%) were misidentified at the species level. DNA sequencing identified 855 NTM isolates from liquid cultures, comprising 316 isolates of rapidly growing mycobacteria (RGM) and 539 isolates of slow-growing mycobacteria (SGM). Using the Vitek MS system, the RGM integral identification rate (276/316 [87.34%]) was higher than the SGM rate (381/539 [70.69%]) (P < 0.01). It was also higher than the SGM rate for all MGIT report-positive periods. These results indicate that the Vitek MS v3.0 system can rapidly identify NTM species from liquid cultures. Further validation using molecular techniques is required. IMPORTANCE Rapid and accurate identification of nontuberculous mycobacteria (NTM) is essential for diagnosis, appropriate therapy, and infection control. Vitek MS v3.0 matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and reliable method for identifying mycobacteria in clinical laboratories. This study reported a clinical validation of the Vitek MS V3.0 system for identification of NTM isolates from 855 MGIT-positive liquid cultures which contained relatively large NTM types. Vitek MS v3.0 showed a promising rate for identification NTM isolates in positive liquid cultures. Vitek MS v3.0 had a better performance with RGM than with SGM. Vitek MS v3.0 results included "unidentified" or "misidentified" NTM isolates, which would also serve as an important reference for future optimization of this system. Vitek MS v3.0 represented a valuable technique for NTM identification from positive liquid cultures.
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24
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Elbehiry A, Aldubaib M, Abalkhail A, Marzouk E, ALbeloushi A, Moussa I, Ibrahem M, Albazie H, Alqarni A, Anagreyyah S, Alghamdi S, Rawway M. How MALDI-TOF Mass Spectrometry Technology Contributes to Microbial Infection Control in Healthcare Settings. Vaccines (Basel) 2022; 10:1881. [PMID: 36366389 PMCID: PMC9699604 DOI: 10.3390/vaccines10111881] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/01/2022] [Accepted: 11/07/2022] [Indexed: 08/01/2023] Open
Abstract
Healthcare settings have been utilizing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) since 2010. MALDI-TOF MS has various benefits over the conventional method of biochemical identification, including ease of use, speed, accuracy, and low cost. This approach can solve many of the obstacles to identifying bacteria, fungi and viruses. As technology advanced, more and more databases kept track of spectra, allowing species with similar morphological, genotypic, and biochemical traits to be identified. Using MALDI-TOF MS for identification has become more accurate and quicker due to advances in sample preparation and database enrichment. Rapid sample detection and colony identification using MALDI-TOF MS have produced promising results. A key application of MALDI-TOF MS is quickly identifying highly virulent and drug-resistant diseases. Here, we present a review of the scientific literature assessing the effectiveness of MALDI-TOF MS for locating clinically relevant pathogenic bacteria, fungi, and viruses. MALDI-TOF MS is a useful strategy for locating clinical pathogens, however, it also has some drawbacks. A small number of spectra in the database and inherent similarities among organisms can make it difficult to distinguish between different species, which can result in misidentifications. The majority of the time additional testing may correct these problems, which happen very seldom. In conclusion, infectious illness diagnosis and clinical care are being revolutionized by the use of MALDI-TOF MS in the clinical microbiology laboratory.
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Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32511, Egypt
| | - Musaad Aldubaib
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Eman Marzouk
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Ahmad ALbeloushi
- Al Bukayriyah General Hospital, Qassim, Al Bukayriyah 52725, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mai Ibrahem
- Department of Public Health, College of Applied Medical Science, King Khalid University, Abha 61421, Saudi Arabia
- Department of Aquatic Animal Medicine and Management, Faculty of Veterinary Medicine, Cairo University, Cairo 12211, Egypt
| | - Hamad Albazie
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Abdullah Alqarni
- Department of Support Service, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Sulaiman Anagreyyah
- Department of Preventive Medicine, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Saleh Alghamdi
- Department of Biomedical Engineering, King Fahad Armed Hospital, Jeddah 23311, Saudi Arabia
| | - Mohammed Rawway
- Biology Department, College of Science, Jouf University, Sakaka 42421, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, AL-Azhar University, Assiut 71524, Egypt
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25
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Evaluation of MALDI Biotyper Mycobacteria Library for Identification of Nontuberculous Mycobacteria. J Clin Microbiol 2022; 60:e0021722. [PMID: 35969171 PMCID: PMC9491183 DOI: 10.1128/jcm.00217-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Bruker Biotyper matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) platform was assessed on its ability to accurately identify 314 nontuberculous mycobacteria (NTM) representing 73 species. All NTM isolates, representing 183 rapidly growing and 131 slowly growing organisms, were previously identified by Sanger DNA sequencing of the full-length 16S rRNA gene, and region V of the rpoB gene. An optimized version of the Bruker bead-beating procedure for protein extraction of NTM isolates was used to ensure high quality spectra for all NTM isolates, including less frequently encountered species. NTM spectra were analyzed using Bruker's research use only, Mycobacteria Library v6.0, supplemented by the MicrobeNet database. Identification of NTM by MALDI-TOF had an accuracy of 94% (296/314). The identification accuracy for rapidly growing mycobacteria was higher at 99% (182/183) than it was for slowly growing mycobacteria at 87% (114/131). While MALDI-TOF performed well against Sanger sequencing of the 16S rRNA gene alone, there were 11 species that required additional sequencing of rpoB. Most discrepancies between MALDI-TOF and sequencing results are likely due to underrepresentation of some species in the libraries used. Overall, the results of this study support Bruker's MALDI-TOF platform as an accurate and reliable method for the identification of NTM.
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26
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A Case of Fungemia Caused by Postoperative Chronic Lumbar Intervertebral Disc Infection. Case Rep Surg 2022; 2022:8311278. [PMID: 35978861 PMCID: PMC9377923 DOI: 10.1155/2022/8311278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/28/2022] [Accepted: 07/05/2022] [Indexed: 12/02/2022] Open
Abstract
Postoperative surgical site infection is one of the serious postoperative complications of spine surgery, especially fungal infections. Late-stage surgical site fungal infections often lack typical clinical symptoms and have a variable clinical presentation. In this case, the patient was a senior patient with usually only tolerable pain and discomfort, which was detected 2 years after the first surgery. Such cases are even rarer for fungal bloodstream infections caused by delayed postoperative chronic fungal osteomyelitis and deserve further study for early identification and intervention to minimize harm.
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27
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Rindi L, Puglisi V, Franconi I, Fais R, Lupetti A. Rapid and Accurate Identification of Nontuberculous Mycobacteria Directly from Positive Primary MGIT Cultures by MALDI-TOF MS. Microorganisms 2022; 10:microorganisms10071447. [PMID: 35889166 PMCID: PMC9317365 DOI: 10.3390/microorganisms10071447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/08/2022] [Accepted: 07/16/2022] [Indexed: 11/16/2022] Open
Abstract
Over the last years, nontuberculous mycobacteria (NTM) have emerged as important human pathogens. Accurate and rapid mycobacterial species identification is needed to successfully diagnose, treat, and manage infections caused by NTM. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, MALDI-TOF MS, was demonstrated to effectively identify mycobacteria isolates subcultured from solid or liquid media rather than new positive cultures. The present study aims to develop a new extraction protocol to yield rapid and accurate identification of NTM from primary MGIT cultures by MALDI-TOF MS. A total of 60 positive MGIT broths were examined by the Bruker Biotyper system with Mycobacteria Library v. 2.0 (Bruker Daltonics GmbH & Co. KG., Bremen, Germany). The results were compared with those obtained by the molecular method, line probe assay GenoType Mycobacterium CM/AS/NTM-DR. All samples were concordantly identified by MALDI-TOF MS and the molecular test for all the tested mycobacteria. Fifty-seven (95%) MGIT positive cultures for NTM from clinical samples had a MALDI-TOF MS analysis score S ≥ 1.8. Although a small number of strains and a limited diversity of mycobacterial species were analysed, our results suggest that MALDI-TOF MS could represent a promising routine diagnostic tool for identifying mycobacterial species directly from primary liquid culture.
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Affiliation(s)
- Laura Rindi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, 56126 Pisa, Italy; (I.F.); (A.L.)
- Correspondence: author:
| | - Vincenzo Puglisi
- SD Microbiologia Micologica, Azienda Ospedaliero-Universitaria Pisana, 56126 Pisa, Italy; (V.P.); (R.F.)
| | - Iacopo Franconi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, 56126 Pisa, Italy; (I.F.); (A.L.)
| | - Roberta Fais
- SD Microbiologia Micologica, Azienda Ospedaliero-Universitaria Pisana, 56126 Pisa, Italy; (V.P.); (R.F.)
| | - Antonella Lupetti
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, 56126 Pisa, Italy; (I.F.); (A.L.)
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28
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Surgical site infections by atypical mycobacteria: prevalence and species characterization using MALDI-TOF and molecular LCD chip array. Infection 2022; 50:1557-1563. [PMID: 35716342 PMCID: PMC9705499 DOI: 10.1007/s15010-022-01864-1] [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: 02/25/2022] [Accepted: 05/24/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Surgical site infection (SSI) is a post-operative complication of high concern with adverse impact on patient prognosis and public health systems. Recently, SSI pathogens have experienced a change in microbial profile with increasing reports of non-tuberculous mycobacteria (NTM) as important pathogens. AIM of the study The study aimed to detect the prevalence of NTM among cases with SSIs and describe their species using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) and PCR-based microarray. METHODS The study was conducted with 192 pus samples collected from patients with SSI. Mycobacterial investigations were done in the form of Ziehl-Neelsen (ZN) smears for acid-fast bacilli, automated mycobacterial culture to isolate mycobacteria, followed by immunochromatography test to predict NTM. NTM-positive cultures were tested by MALDI -TOF MS and PCR-based microarray to reach species-level identification. RESULTS Mycobacterial growth was found in 11/192 samples (5.7%) and identified as 4 NTM and 7 M. tuberculosis isolates with prevalence of 2.1% and 3.64%, respectively. The NTM species were described by MALDI-TOF as M. abscessus, M. porcinum, M. bacteremicum, and M. gordonae. Microarray agreed with MALDI-TOF in identifying one isolate (M. abscessus), while two isolates were classified as belonging to broad groups and one isolate failed to be identified. CONCLUSIONS The prevalence of NTM among SSI was found to be low, yet have to be considered in the diagnosis of mycobacteria. Employing advanced technologies in diagnosis is recommended to guide for appropriate treatment.
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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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30
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López Medrano R, Burgos Asurmendi I, Rivero Lezcano OM. A rapid proteomic system (MALDI-TOF) for nontuberculous-mycobacteria identification. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:385-387. [PMID: 35537995 DOI: 10.1016/j.eimce.2022.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/28/2022]
Abstract
Proteomic techniques relaying upon mass spectrometry (MALDI_TOF) applied to nontuberculous mycobacteria (NTM) identification, constitute a difficult goal. Cell wall structure features complicates the protein extraction procedure. A total of 106 isolates belonging to a variety of MNTs species isolated from clinical samples taken at the Complejo Asistencial Universitario de León for a two years period (2019-20) were identified following a simplified method (MALDI-TOF Biotyper Bruker®) developped in our laboratory. The resultant identification was compared to a parallel one ruled on the Centro de Referencia de Majadahonda. A total of 22different MNTs species were tested, obtaining an agreement of 92,45%. Only 8 minor discrepancies between species belonging to same taxonomic group of MNTs were detected. The score obtained in the 67.92% of the cases was higher than 1.8. A time-saving of 24min compared to the manufacturer's proceeding was achieved.
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Affiliation(s)
- Ramiro López Medrano
- Servicio de Microbiología, Complejo Asistencial Universitario de León, León, Spain.
| | - Isabel Burgos Asurmendi
- Servicio de Anestesiología y Reanimación, Complejo Asistencial Universitario de León, León, Spain
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31
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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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Chew KL, Soh P, Octavia S, Teo J. Identification of Mycobacterium abscessus to subspecies level with Bruker MALDI Biotyper. Pathology 2022; 54:795-797. [DOI: 10.1016/j.pathol.2021.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 11/28/2022]
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Lorente-Leal V, Liandris E, Bezos J, Pérez-Sancho M, Romero B, de Juan L. MALDI-TOF Mass Spectrometry as a Rapid Screening Alternative for Non-tuberculous Mycobacterial Species Identification in the Veterinary Laboratory. Front Vet Sci 2022; 9:827702. [PMID: 35155660 PMCID: PMC8831857 DOI: 10.3389/fvets.2022.827702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/03/2022] [Indexed: 11/30/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are difficult to identify by biochemical and genetic methods due to their microbiological properties and complex taxonomy. The development of more efficient and rapid methods for species identification in the veterinary microbiological laboratory is, therefore, of great importance. Although MALDI-TOF Mass Spectrometry (MS) has become a promising tool for the identification of NTM species in human clinical practise, information regarding its performance on veterinary isolates is scarce. This study assesses the capacity of MALDI-TOF MS to identify NTM isolates (n = 75) obtained from different animal species. MALDI-TOF MS identified 76.0% (n = 57) and 4% (n = 3) of the isolates with high and low confidence, respectively, in agreement with the identification achieved by Sanger sequencing of housekeeping genes (16S rRNA, hsp65, and rpoB). Thirteen isolates (17.3%) were identified by Sanger sequencing to the complex level, indicating that these may belong to uncharacterised species. MALDI-TOF MS approximated low confidence identifications toward closely related mycobacterial groups, such as the M. avium or M. terrae complexes. Two isolates were misidentified due to a high similarity between species or due to the lack of spectra in the database. Our results suggest that MALDI-TOF MS can be used as an effective alternative for rapid screening of mycobacterial isolates in the veterinary laboratory and potentially for the detection of new NTM species. In turn, Sanger sequencing could be implemented as an additional method to improve identifications in species for which MALDI-TOF MS identification is limited or for further characterisation of NTM species.
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Affiliation(s)
- Víctor Lorente-Leal
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Emmanouil Liandris
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
| | - Javier Bezos
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Marta Pérez-Sancho
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Beatriz Romero
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
- *Correspondence: Beatriz Romero
| | - Lucía de Juan
- VISAVET Health Surveillance Center, Universidad Complutense de Madrid, Madrid, Spain
- Animal Health Department, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, Madrid, Spain
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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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Microbial Identification in the Clinical Microbiology Laboratory Using MALDI-TOF-MS. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2420:207-216. [PMID: 34905176 DOI: 10.1007/978-1-0716-1936-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
MALDI-TOF mass spectrometry has been applied with huge success to the identification of cultured microorganisms in clinical microbiology laboratories where it has become the reference method because it is simple, fast, and highly reproducible. We describe the different procedures used in the routine for pathogen identification using the Bruker MALDI Biotyper® system.
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Nishii Y, Furuhashi K, Nakamura S, Nishio M, Nakamura Y, Ushiro K, Ito K, Sakaguchi T, Suzuki Y, Fujiwara K, Yasuma T, Kobayashi T, D'Alessandro-Gabazza C, Gabazza EC, Taguchi O, Hataji O. The Potential of Digital Polymerase Chain Reaction for Improving Diagnostic Yield of Nontuberculous Mycobacteria Pulmonary Disease. Infect Drug Resist 2021; 14:5079-5087. [PMID: 34880633 PMCID: PMC8646858 DOI: 10.2147/idr.s338165] [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: 09/07/2021] [Accepted: 10/30/2021] [Indexed: 11/23/2022] Open
Abstract
Introduction Many patients with nontuberculous mycobacteria pulmonary disease are asymptomatic. The disease diagnosis is confirmed in only a small proportion of patients with radiological findings suspicious for nontuberculous mycobacteria pulmonary disease. Thus, many patients remained undiagnosed. Here, we evaluated the diagnostic value of digital polymerase chain reaction (PCR) in nontuberculous mycobacteria pulmonary disease. Methods We prospectively evaluated 123 patients with radiological findings suspicious for nontuberculous mycobacteria pulmonary disease. Digital PCR was performed using bronchial lavage fluid, sputum, saliva, blood, and urine. Results The culture of bronchial washing fluid was positive for nontuberculous mycobacteria in 53 patients and negative in 70. The positive detection rate of nontuberculous mycobacteria by digital PCR in patients with positive culture (n = 53) was as follows: bronchial lavage fluid 100%, sputum 62.9%, saliva 41.5%, blood 7.5%, and urine 3.8%. All patients with two or more positive partitions for nontuberculous mycobacteria in the digital PCR of bronchial lavage fluid showed nontuberculous mycobacteria growth in the bronchial lavage fluid culture. The digital PCR analysis of the bronchial lavage fluid showed a high sensitivity (100%), specificity (85.7%), positive predictive value (84.1%), negative predictive value (100%), and a high concordance rate (91.9%) with the bronchial lavage fluid culture results. In addition, the culture of bronchial lavage fluid was positive for nontuberculous mycobacteria in patients with two or more positive partitions in the digital PCR of sputum and saliva with a combined positive predictive value of 81.1%. Conclusion Digital PCR analysis of nontuberculous mycobacteria in bronchial lavage fluid shows a high concordance rate with the bronchial lavage fluid culture results and a high positive predictive value using both sputum and saliva, suggesting the potential usefulness of dPCR for diagnosis of nontuberculous mycobacteria pulmonary disease in clinical practice.
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Affiliation(s)
- Yoichi Nishii
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Mie, Japan
| | - Kazuki Furuhashi
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Mie, Japan
| | - Saki Nakamura
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Mie, Japan
| | - Miho Nishio
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Mie, Japan
| | - Yuki Nakamura
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Mie, Japan
| | - Kengo Ushiro
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Mie, Japan
| | - Kentaro Ito
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Mie, Japan
| | - Tadashi Sakaguchi
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Mie, Japan
| | - Yuta Suzuki
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Mie, Japan
| | - Kentaro Fujiwara
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Mie, Japan
| | - Taro Yasuma
- Department of Immunology, Faculty and Graduate School of Medicine, Mie University, Tsu-city, Mie, Japan
| | - Tetsu Kobayashi
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu-city, Mie, Japan
| | | | - Esteban C Gabazza
- Department of Immunology, Faculty and Graduate School of Medicine, Mie University, Tsu-city, Mie, Japan
| | - Osamu Taguchi
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Mie, Japan
| | - Osamu Hataji
- Respiratory Center, Matsusaka Municipal Hospital, Matsusaka, Mie, Japan
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Koyama T, Funakoshi Y, Imamura Y, Nishimura S, Fujishima Y, Toyoda M, Kiyota N, Tanino H, Minami H. Device-related Mycobacterium mageritense Infection in a Patient Treated with Nivolumab for Metastatic Breast Cancer. Intern Med 2021; 60:3485-3488. [PMID: 33994435 PMCID: PMC8627816 DOI: 10.2169/internalmedicine.6550-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Treatment with anti-programmed cell death-1 (PD-1) antibodies improves the anti-cancer immune response and can provide a meaningful clinical benefit to cancer patients. However, this treatment can result in specific autoimmune toxicities, termed immune-related adverse events (irAEs). Although irAEs are well recognized, the development of infectious diseases due to this treatment is not often observed. Some recent reports have indicated that patients who receive anti-PD-1 antibodies are at a higher risk for tuberculosis than others. However, reports on nontuberculous mycobacterial infection during anti-PD-1 antibody treatment are still rare. We herein report the first case of Mycobacterium mageritense infection during anti-PD-1 antibody treatment.
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Affiliation(s)
- Taiji Koyama
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Japan
| | - Yohei Funakoshi
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Japan
| | - Yoshinori Imamura
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Japan
| | - Sho Nishimura
- Division of Infectious Diseases, Department of Medicine, Kobe University Hospital, Japan
| | - Yoshimi Fujishima
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Japan
| | - Masanori Toyoda
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Japan
| | - Naomi Kiyota
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Japan
- Cancer Center, Kobe University Hospital and Graduate School of Medicine, Japan
| | - Hirokazu Tanino
- Division of Breast and Endocrine Surgery, Department of Surgery, Kobe University Hospital and Graduate School of Medicine, Japan
| | - Hironobu Minami
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Japan
- Cancer Center, Kobe University Hospital and Graduate School of Medicine, Japan
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Lephart P, LeBar W, Newton D. Behind Every Great Infection Prevention Program is a Great Microbiology Laboratory: Key Components and Strategies for an Effective Partnership. Infect Dis Clin North Am 2021; 35:789-802. [PMID: 34362544 DOI: 10.1016/j.idc.2021.04.012] [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: 11/18/2022]
Abstract
A great clinical microbiology laboratory supporting a great infection prevention program requires focusing on the following services: rapid and accurate identification of pathogens associated with health care-associated infections; asymptomatic surveillance for health care-acquired pathogens before infections arise; routine use of broad and flexible antimicrobial susceptibility testing to direct optimal therapy; implementation of epidemiologic tracking tools to identify outbreaks; development of clear result communication with interpretative comments for clinicians. These goals are best realized in a collaborative relationship with the infection prevention program so that both can benefit from the shared priorities of providing the best patient care.
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Affiliation(s)
- Paul Lephart
- Clinical Microbiology Laboratory, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA.
| | - William LeBar
- Clinical Microbiology Laboratory, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA
| | - Duane Newton
- NaviDx Consulting, Department of Pathology, University of Michigan Medical School, 2800 Plymouth Road Building 36-1221-52, Ann Arbor, MI 48109-2800, USA
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López Medrano R, Burgos Asurmendi I, Rivero Lezcano OM. A rapid proteomic system (MALDI-TOF) for nontuberculous-mycobacteria identification. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00203-2. [PMID: 34266677 DOI: 10.1016/j.eimc.2021.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 11/24/2022]
Abstract
Proteomic techniques relaying upon mass spectrometry (MALDI_TOF) applied to nontuberculous mycobacteria (NTM) identification, constitute a difficult goal. Cell wall structure features complicates the protein extraction procedure. A total of 106 isolates belonging to a variety of MNTs species isolated from clinical samples taken at the Complejo Asistencial Universitario de León for a two years period (2019-20) were identified following a simplified method (MALDI-TOF Biotyper Bruker®) developped in our laboratory. The resultant identification was compared to a parallel one ruled on the Centro de Referencia de Majadahonda. A total of 22 different MNTs species were tested, obtaining an agreement of 91,5%. Only 9 minor discrepancies between species belonging to the same taxonomic group of MNTs were detected. The score obtained in the 67.92% of the cases was higher than 1.8. A time-saving of 24 minutes compared to the manufacturer's proceeding was achieved.
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Affiliation(s)
- Ramiro López Medrano
- Servicio de Microbiología. Complejo Asistencial Universitario de León, León, España.
| | - Isabel Burgos Asurmendi
- Servicio de Anestesiología y Reanimación. Complejo Asistencial Universitario de León, León, España
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Naia L, Rabadão T, Teixeira M, Ferreira F, Pinto S, Ferreira R, Eulálio M. Heart failure as a first sign of disseminated tuberculosis. J Community Hosp Intern Med Perspect 2021; 11:558-562. [PMID: 34211669 PMCID: PMC8221148 DOI: 10.1080/20009666.2021.1936949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Tuberculous pericarditis is a rare extra-pulmonary manifestation of tuberculosis observed mainly in developed countries. It usually presents with concomitant tuberculous infection at a different site and, due to the lack of clinical specificity, diagnosis can be difficult. Thus, a diagnostic delay is frequent, entailing increased morbidity and mortality. The authors present a case of disseminated tuberculosis with predominantly cardiac symptoms with multiple negative samples for Mycobacterium tuberculosis, which evolved to constrictive pericarditis. With this case report, the authors emphasize the demand for a high index of suspicion for achieving a diagnosis and the importance of a multidisciplinary approach.
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Affiliation(s)
- Leonor Naia
- Internal Medicine Department, Centro Hospitalar Do Baixo-Vouga, Aveiro, Portugal
| | - Tiago Rabadão
- Internal Medicine Department, Centro Hospitalar Do Baixo-Vouga, Aveiro, Portugal
| | - Mariana Teixeira
- Internal Medicine Department, Centro Hospitalar Do Baixo-Vouga, Aveiro, Portugal
| | - Filipa Ferreira
- Internal Medicine Department, Centro Hospitalar Do Baixo-Vouga, Aveiro, Portugal
| | - Sara Pinto
- Internal Medicine Department, Centro Hospitalar Do Baixo-Vouga, Aveiro, Portugal
| | - Raquel Ferreira
- Cardiology Department, Centro Hospitalar Do Baixo-Vouga, Aveiro, Portugal
| | - Margarida Eulálio
- Internal Medicine Department, Centro Hospitalar Do Baixo-Vouga, Aveiro, Portugal
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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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Liu CF, Song YM, He WC, Liu DX, He P, Bao JJ, Wang XY, Li YM, Zhao YL. Nontuberculous mycobacteria in China: incidence and antimicrobial resistance spectrum from a nationwide survey. Infect Dis Poverty 2021; 10:59. [PMID: 33926548 PMCID: PMC8082609 DOI: 10.1186/s40249-021-00844-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Information on the prevalence and resistance spectrum of nontuberculous mycobacteria (NTM) in China is mainly based on regional or local data. To estimate the proportion of NTM cases in China, a national survey of NTM pulmonary disease was carried out based on acid-fast positive sputum samples collected in 2013. METHODS Sputum samples collected from enrolled presumptive cases in 72 nationwide tuberculosis surveillance sites from the 31 provinces in the mainland of China were cultured using L-J medium at the National tuberculosis reference laboratory (NTRL). MALDI-TOF MS identified the species of re-cultured strains, and minimal inhibitory concentrations (MICs) were determined to evaluate the drug susceptibility of NTM isolates. Data analysis used statistical software SPSS version 22.0 for Windows statistical package. RESULTS Of 4917 mycobacterial isolates cultured, 6.4% [317/4917, 95% confidence interval (CI) 5.8%-7.2%] were confirmed as NTM, among which 7.7% (287/3709, 95% CI 6.9%-8.6%) were from the southern region. In inland and coastal China, 87.7% (95% CI 78.7%-93.2%) and 50.0% (95% CI 43.7%-56.3%) of isolates, respectively, were slow-growing mycobacteria (SGM), with the remaining rapid growing mycobacteria (RGM). A total of 29 species were detected, Mycobacterium abscessus had higher clarithromycin-inducible resistance rates than M. massiliense (65.67% vs 2.22%). M. kansasii presented lower resistance rates in linezolid and moxifloxacin than M. avium-intracellulare complex (3.23% vs 66.67%, 0 vs 47.22%) and other SGM (3.23% vs 38%, 0 vs 26%). CONCLUSIONS More NTM pulmonary disease was observed in the south and coastal China (P < 0.01). SGM was widely distributed, and more RGM are present in southern and coastal China (P < 0.01). The antimicrobial resistance spectrum of different NTM species was significantly different and accurate species identification would be facilitated to NTM pulmonary disease treatment.
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Affiliation(s)
- Chun-Fa Liu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing102206, China
| | - Yi-Meng Song
- National Center of Gerontology, Beijing Hospital, Dongdandahua Road 1, Dongcheng, Beijing, 100730, China
| | - Wen-Cong He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Dong-Xin Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Guangdong, 518112, China
| | - Ping He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jing-Jing Bao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Inner Mongolia Medical University, Inner Mongolia, 010110, China
| | - Xin-Yang Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Basic Medicine, Harbin Medical University, Heilongjiang, 150081, China
| | - Yan-Ming Li
- National Center of Gerontology, Beijing Hospital, Dongdandahua Road 1, Dongcheng, Beijing, 100730, China.
| | - Yan-Lin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing102206, China.
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MALDI-TOF mass spectrometry in the 21st century clinical microbiology laboratory. Enferm Infecc Microbiol Clin 2021; 39:192-200. [DOI: 10.1016/j.eimc.2020.02.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/09/2020] [Accepted: 02/19/2020] [Indexed: 01/12/2023]
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Oshima K, Niinuma Y, Saito H, Baba H, Kanamori H, Aoyagi T, Tokuda K, Kaku M. Pulmonary infection caused by Mycobacterium marinum in a patient with anorexia nervosa. ERJ Open Res 2021; 7:00782-2020. [PMID: 33748256 PMCID: PMC7957289 DOI: 10.1183/23120541.00782-2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/29/2021] [Indexed: 11/26/2022] Open
Abstract
The global incidence of nontuberculous mycobacterial pulmonary disease (NTM-PD) has been increasing [1]. Recently popularised microbiology tests, including 16S rRNA sequencing and matrix-assisted laser desorption ionisation–time-of-flight mass spectrometry, have made it possible to identify rare nonmycobacterial species previously unidentifiable using conventional methods [2, 3]. Transmission of Mycobacterium marinum to humans is mainly through direct contact with domesticated fish or through pre-existing wounds or abrasions on limbs exposed to contaminated water [4]. M. marinum causes swimming pool or fish tank granuloma [4]. The organism grows well at 30–32°C, but poorly or not at all at 37°C [4]. Most M. marinum infections do not invade deeper than the superficial cooler regions of the skin, and pulmonary infections are rarely reported [4]. Mycobacterium marinum can cause pulmonary infection and can grow at ≤32°C. Physicians should consider M. marinum when examining patients with pulmonary infection and low body temperature or anorexia nervosa, and grow the specimen at ≤32°C.https://bit.ly/3jkzBeq
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Affiliation(s)
- Kengo Oshima
- Dept of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.,Dept of Intelligent Network for Infection Control, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yukari Niinuma
- Ohmichi Internal Medicine and Respiratory Clinic, Sapporo, Japan
| | - Hajime Saito
- Hiroshima Environment & Health Association, Health Science Center, Hiroshima, Japan
| | - Hiroaki Baba
- Dept of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.,Dept of Intelligent Network for Infection Control, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hajime Kanamori
- Dept of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.,Dept of Intelligent Network for Infection Control, Tohoku University Graduate School of Medicine, Sendai, Japan.,Division of Infection Control, Tohoku University Hospital, Sendai, Japan
| | - Tetsuji Aoyagi
- Dept of Infectious Diseases, Internal Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.,Dept of Intelligent Network for Infection Control, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Koichi Tokuda
- Dept of Intelligent Network for Infection Control, Tohoku University Graduate School of Medicine, Sendai, Japan.,Division of Infection Control, Tohoku University Hospital, Sendai, Japan
| | - Mitsuo Kaku
- Dept of Infectious Disease, Tohoku Medical and Pharmaceutical University, Sendai, Japan
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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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Banaei N, Musser KA, Salfinger M, Somoskovi A, Zelazny AM. Novel Assays/Applications for Patients Suspected of Mycobacterial Diseases. Clin Lab Med 2020; 40:535-552. [DOI: 10.1016/j.cll.2020.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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47
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Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. A high-stringency blueprint of the human proteome. Nat Commun 2020; 11:5301. [PMID: 33067450 PMCID: PMC7568584 DOI: 10.1038/s41467-020-19045-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.
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Affiliation(s)
- Subash Adhikari
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Edouard C Nice
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
- Faculty of Medicine, Nursing and Health Sciences, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Eric W Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Lydie Lane
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218, USA
| | - Stephen R Pennington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Young-Ki Paik
- Yonsei Proteome Research Center, 50 Yonsei-ro, Sudaemoon-ku, Seoul, 120-749, South Korea
| | | | - Fernando J Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, 28049, Madrid, Spain
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Jennifer E Van Eyk
- Cedars Sinai Medical Center, Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Los Angeles, CA, 90048, USA
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Cecilia Lindskog
- Rudbeck Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, 75185, Uppsala, Sweden
| | - Daniel W Chan
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Amos Bairoch
- Faculty of Medicine, SIB-Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Michel-Servet 1, 1211, Geneva, Switzerland
| | - James C Waddington
- UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine, University College Dublin, Dublin, Ireland
| | - Joshua L Justice
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Markus Kostrzewa
- Bruker Daltonik GmbH, Microbiology and Diagnostics, Fahrenheitstrasse, 428359, Bremen, Germany
| | - Peipei Ping
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Rebekah L Gundry
- CardiOmics Program, Center for Heart and Vascular Research, Division of Cardiovascular Medicine and Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Peter Stewart
- Department of Chemical Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | | | - Sudhir Srivastava
- Cancer Biomarkers Research Branch, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Suite 5E136, Rockville, MD, 20852, USA
| | - Fabio C S Nogueira
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Gilberto B Domont
- Proteomics Unit and Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro, Av Athos da Silveria Ramos, 149, 21941-909, Rio de Janeiro, RJ, Brazil
| | - Yves Vandenbrouck
- University of Grenoble Alpes, Inserm, CEA, IRIG-BGE, U1038, 38000, Grenoble, France
| | - Maggie P Y Lam
- Departments of Medicine-Cardiology and Biochemistry and Molecular Genetics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
- Consortium for Fibrosis Research and Translation, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Sara Wennersten
- Division of Cardiology, Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Juan Antonio Vizcaino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Marc Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 17121, Solna, Sweden
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, Mail Code 0404, La Jolla, CA, 92093-0404, USA
| | | | - Susan T Weintraub
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center San Antonio, UT Health, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Charles Pineau
- University of Rennes, Inserm, EHESP, IREST, UMR_S 1085, F-35042, Rennes, France
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
| | - Seong Beom Ahn
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Magnus Palmblad
- Leiden University Medical Center, Leiden, 2333, The Netherlands
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA
| | - Ruedi Aebersold
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA, 98109, USA
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Mark S Baker
- Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia.
- Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA.
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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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Development and Validation of an In-House Library for Filamentous Fungi Identification by MALDI-TOF MS in a Clinical Laboratory in Medellin (Colombia). Microorganisms 2020; 8:microorganisms8091362. [PMID: 32899976 PMCID: PMC7563289 DOI: 10.3390/microorganisms8091362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 08/30/2020] [Accepted: 09/04/2020] [Indexed: 12/15/2022] Open
Abstract
Identification of filamentous fungi by conventional phenotypic methods are time-consuming, and a correct identification at the species level is prone to errors. Therefore, a more accurate and faster time-to-results, and cost-effective technique, is required, such as the Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). In this study, we describe the development of an in-house spectra library for the identification of filamentous fungi frequently isolated from patients with infections. An in-house spectra library was constructed using 14 reference strains grown in solid medium. Clinical isolates were identified either by the in-house spectra library or the Biotyper commercial library from Bruker Daltonics. Fungal identification was carried following the Biotyper’s established scores: ≤1.699: not reliably identified (NRI); 1.700–1.999: genus-level; ≥2.000: species-level. Clinical isolates were identified, with the in-house library, at species- and genus-level at 88.70% (55) and 3.22% (2), respectively. While 4.80% (3) was NRI and 3.22% (2) was discrepant concerning sequencing. On the contrary, identification up to species and genus-level with the commercial library was 44.44% (16) and 22.22% (8), respectively. NRI and the discrepancy was 30.55% (11) and 2.77% (1), respectively. For the reaming 26 isolates, 16 from Neoscytalidium dimidiatum and 10 from Sporothrix spp., respectively, the absence of spectrum and the specific spectra within the Sporothrix complex in the commercial library resulted in the inability to obtain an identification. In conclusion, the current results advocate the importance that each clinical microbiological laboratory needs to develop an ad hoc library associated with the MALDI-TOF MS fungal identification to overcome the limitations of the available commercial libraries.
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