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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 UniversitéParisFrance
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Département de BactériologieGroupe Hospitalier Universitaire, Sorbonne Université, HôpitalParisFrance
| | - Lise Bigey
- U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi‐Paris)Sorbonne UniversitéParisFrance
- DER (Département d'Enseignement et de Recherche) de Biologie, ENS Paris‐SaclayUniversité Paris‐SaclayGif‐sur‐YvetteFrance
| | - Quentin Giai‐Gianetto
- Institut PasteurUniversité Paris Cité, Bioinformatics and Biostatistics HUBParisFrance
- Institut PasteurUniversité Paris Cité, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR CNRS 2024ParisFrance
| | - Gautier Pierrat
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Département de BactériologieGroupe Hospitalier Universitaire, Sorbonne Université, HôpitalParisFrance
| | - Noshine Mohammad
- Inserm, Institut Pierre‐Louis d'Epidémiologie et de Santé Publique, IPLESP, AP‐HP, Groupe Hospitalier Pitié‐Salpêtrière, Service de Parasitologie‐ MycologieSorbonne UniversitéParisFrance
| | - Faiza Mougari
- Service de Mycobactériologie spécialisée et de référence, Centre National de Référence des Mycobactéries (Laboratoire associé), APHP GHU NordUniversité Paris Cité, INSERM IAME UMRParisFrance
| | - Renaud Piarroux
- Inserm, Institut Pierre‐Louis d'Epidémiologie et de Santé Publique, IPLESP, AP‐HP, Groupe Hospitalier Pitié‐Salpêtrière, Service de Parasitologie‐ MycologieSorbonne UniversitéParisFrance
| | - Nicolas Veziris
- U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi‐Paris)Sorbonne UniversitéParisFrance
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris), Département de BactériologieGroupe Hospitalier Universitaire, Sorbonne Université, HôpitalParisFrance
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris)Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux AntituberculeuxParisFrance
| | - Alexandra Aubry
- U1135, Centre d'Immunologie et des Maladies Infectieuses (Cimi‐Paris)Sorbonne UniversitéParisFrance
- AP‐HP, Sorbonne Université (Assistance Publique Hôpitaux de Paris)Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux AntituberculeuxParisFrance
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Takei S, Teramoto K, Sekiguchi Y, Ihara H, Tohya M, Iwamoto S, Tanaka K, Khasawneh A, Horiuchi Y, Misawa S, Naito T, Kirikae T, Tada T, Tabe Y. Identification of Mycobacterium abscessus using the peaks of ribosomal protein L29, L30 and hemophore-related protein by MALDI-MS proteotyping. Sci Rep 2024; 14:11187. [PMID: 38755267 PMCID: PMC11099050 DOI: 10.1038/s41598-024-61549-7] [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: 01/19/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Mycobacteroides (Mycobacterium) abscessus, which causes a variety of infectious diseases in humans, is becoming detected more frequently in clinical specimens as cases are spreading worldwide. Taxonomically, M. abscessus is composed of three subspecies of M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense, with different susceptibilities to macrolides. In order to identify rapidly these three subspecies, we determined useful biomarker proteins, including ribosomal protein L29, L30, and hemophore-related protein, for distinguishing the subspecies of M. abscessus using the matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) profiles. Thirty-three clinical strains of M. abscessus were correctly identified at the subspecies-level by the three biomarker protein peaks. This study ultimately demonstrates the potential of routine MALDI-MS-based laboratory methods for early identification and treatment for M. abscessus infections.
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Affiliation(s)
- Satomi Takei
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Kanae Teramoto
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Analytical and Measurement Instruments Division, Shimadzu Corporation, Kyoto, Japan
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Hiroaki Ihara
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mari Tohya
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, Kyoto, Japan
| | - Abdullah Khasawneh
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuki Horiuchi
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shigeki Misawa
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Clinical Laboratory Technology, Faculty of Medical Science, Juntendo University, Tokyo, Japan
| | - Toshio Naito
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of General Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Teruo Kirikae
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Microbiome Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Tatsuya Tada
- Department of Microbiology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
| | - Yoko Tabe
- Department of Clinical Laboratory Medicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of MALDI-TOF MS Practical Application Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
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Jia Khor M, Broda A, Kostrzewa M, Drobniewski F, Larrouy-Maumus G. An Improved Method for Rapid Detection of Mycobacterium abscessus Complex Based on Species-Specific Lipid Fingerprint by Routine MALDI-TOF. Front Chem 2021; 9:715890. [PMID: 34386482 PMCID: PMC8353234 DOI: 10.3389/fchem.2021.715890] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 06/28/2021] [Indexed: 01/09/2023] Open
Abstract
Rapid diagnostics of bacterial infection is the key to successful recovery and eradication of the disease. Currently, identification of bacteria is based on the detection of highly abundant proteins, mainly ribosomal proteins, by routine MALDI-TOF mass spectrometry. However, relying solely on proteins is limited in subspecies typing for some pathogens. This is the case for, for example, the mycobacteria belonging to the Mycobacterium abscessus (MABS) complex, which is classified into three subspecies, namely, M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense. Being able to detect bacteria accurately and rapidly at the subspecies level could not only reliably identify the pathogen causing the disease but also enable better antibiotic stewardship. For instance, M. abscessus subsp. abscessus and M. abscessus subsp. bolletii possess a functional erm41 (erythromycin ribosomal methylation gene 41) gene, whilst M. abscessus subsp. massiliense does not, resulting in differences in macrolide antibiotic (e.g., clarithromycin and azithromycin) susceptibilities. This presents a challenge for physicians when designing an appropriate treatment regimen. To address this challenge, in addition to proteins, species-specific lipids have now been considered as a game changer in clinical microbiology diagnostics. However, their extraction can be time-consuming, and analysis requires the use of apolar toxic organic solvents (e.g., chloroform). Here, we present a new method to accurately detect species and subspecies, allowing the discrimination of the mycobacteria within the MABS complex and relying on the use of ethanol. We found that a combination of the matrix named super-DHB with 25% ethanol with a bacterial suspension at McFarland 20 gave robust and reproducible data, allowing the discrimination of the bacteria within the MABS complex strains tested in this study (n = 9). Further investigations have to be conducted to validate the method on a larger panel of strains for its use in diagnostic laboratories.
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Affiliation(s)
- Min Jia Khor
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Agnieszka Broda
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | | | - Francis Drobniewski
- Department of Infectious Diseases, Faculty of Medicine, 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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Xiao G, Zhang S, Liang Z, Li G, Fang M, Liu Y, Zhang J, Ou M, He X, Zhang T, Zeng C, Liu L, Zhang G. Identification of Mycobacterium abscessus species and subspecies using the Cas12a/sgRNA-based nucleic acid detection platform. Eur J Clin Microbiol Infect Dis 2020; 39:551-558. [PMID: 31776874 DOI: 10.1007/s10096-019-03757-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/28/2019] [Indexed: 12/26/2022]
Abstract
The rapidly growing mycobacterium Mycobacterium abscessus is a clinically important organism causing pulmonary and skin diseases. The M. abscessus complex is comprised of three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. massiliense, and M. abscessus subsp. bolletii. Here, we aimed to develop a Cas12a/sgRNA-based nucleic acid detection platform to identify M. abscessus species and subspecies. By designing specific sgRNA probes targeting rpoB and erm(41), we demonstrated that M. abscessus could be differentiated from other major mycobacterial species and identified at the subspecies level. Using this platform, a total of 38 clinical M. abscessus isolates were identified, 18 as M. abscessus subsp. abscessus and 20 as M. abscessus subsp. massiliense. We concluded that the Cas12a/sgRNA-based nucleic acid detection platform provides an easy-to-use, quick, and cost-effective approach for identification of M. abscessus species and subspecies.
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Affiliation(s)
- Guohui Xiao
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, 510530, China
| | - Su Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Zhihang Liang
- School of Basic Medical Sciences, Guangdong Medical University, Dongguan, 524023, China
| | - Guanqiang Li
- Department of Laboratory Medicine, Shenzhen Longgang People's Hospital, The Chinese University of Hong Kong, Shenzhen, 518172, China
| | - Mutong Fang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Yaya Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Juanjuan Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Min Ou
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Xing He
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, 510530, China
| | - Changchun Zeng
- Department of Laboratory Medicine, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen, 518110, China
| | - Lei Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, 518112, China.
- School of Basic Medical Sciences, Guangdong Medical University, Dongguan, 524023, China.
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Brown-Elliott BA, Fritsche TR, Olson BJ, Vasireddy S, Vasireddy R, Iakhiaeva E, Alame D, Wallace RJ, Branda JA. Comparison of Two Commercial Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Systems for Identification of Nontuberculous Mycobacteria. Am J Clin Pathol 2019; 152:527-536. [PMID: 31314059 PMCID: PMC6733354 DOI: 10.1093/ajcp/aqz073] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES This multicenter study's aim was to assess the performance of two commercially available matrix-assisted laser desorption/ionization time of flight mass spectrometry systems in identifying a challenge collection of clinically relevant nontuberculous mycobacteria (NTM). METHODS NTM clinical isolates (n = 244) belonging to 23 species/subspecies were identified by gene sequencing and analyzed using Bruker Biotyper with Mycobacterial Library v5.0.0 and bioMérieux VITEK MS with v3.0 database. RESULTS Using the Bruker or bioMérieux systems, 92% and 95% of NTM strains, respectively, were identified at least to the complex/group level; 62% and 57%, respectively, were identified to the highest taxonomic level. Differentiation between members of Mycobacterium abscessus, M fortuitum, M mucogenicum, M avium, and M terrae complexes/groups was problematic for both systems, as was identification of M chelonae for the Bruker system. CONCLUSIONS Both systems identified most NTM isolates to the group/complex level, and many to the highest taxonomic level. Performance was comparable.
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Affiliation(s)
| | - Thomas R Fritsche
- Marshfield Clinic Health System, Marshfield, WI
- University of Wisconsin, La Crosse
| | | | | | | | | | - Diana Alame
- Thomas Jefferson University, Philadelphia, PA
| | | | - John A Branda
- Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, MA
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Huh HJ, Kim SY, Jhun BW, Shin SJ, Koh WJ. Recent advances in molecular diagnostics and understanding mechanisms of drug resistance in nontuberculous mycobacterial diseases. INFECTION GENETICS AND EVOLUTION 2018; 72:169-182. [PMID: 30315892 DOI: 10.1016/j.meegid.2018.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 01/31/2023]
Abstract
Accumulating evidence suggests that human infections caused by nontuberculous mycobacteria (NTM) are increasing worldwide, indicating that NTM disease is no longer uncommon in many countries. As a result of an increasing emphasis on the importance of differential identification of NTM species, several molecular tools have recently been introduced in clinical and experimental settings. These advances have led to a much better understanding of the diversity of NTM species with regard to clinical aspects and the potential factors responsible for drug resistance that influence the different outcomes of NTM disease. In this paper, we review currently available molecular diagnostics for identification and differentiation of NTM species by summarizing data from recently applied methods, including commercially available assays, and their relevant strengths and weaknesses. We also highlight drug resistance-associated genes in clinically important NTM species. Understanding the basis for different treatment outcomes with different causative species and drug-resistance mechanisms will eventually improve current treatment regimens and facilitate the development of better control measures for NTM diseases.
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Affiliation(s)
- Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Su-Young Kim
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Byung Woo Jhun
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea.
| | - Won-Jung Koh
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea.
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Accuracy of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Mycobacteria: a systematic review and meta-analysis. Sci Rep 2018. [PMID: 29515167 PMCID: PMC5841357 DOI: 10.1038/s41598-018-22642-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium species are a significant cause of morbidity and mortality worldwide. The present study was carried out to systematically evaluate the accuracy of Matrix-assisted laser desorption ionization-time of flight mass spectroscopy (MALDI-TOF MS) for the identification of clinical pathogenic mycobacteria. After a rigid selection process, 19 articles involving 2,593 mycobacteria isolates were included. The pooled result agreed with the reference method identification for 85% of the isolates to genus level, with 71% (95% CI of 69% to 72%) correct to the species level. The MALDI-TOF MS correctly identified 92% of the M.tuberculosis isolates (95% CI of 0.87 to 0.96), and 68% of M. bovisisolates (95% CI of 27% to 100%) to the species level. Mycobacterium tuberculosis complex in solid media with reference strains using augmented database showing more accurate identification. The identifying accuracy rate of bioMérieuxVitek MS was slight higher than Bruker MALDI Biotyper (75% vs 72%). However, opposite results were obtained in identifications of M. fortuitum, M. kansasii, M. marinum, and M. terrae with these two systems. In summary, our results demonstrate that application of MALDI-TOF MS in clinical pathogenic mycobacteria identification is less satisfactory to date. Increasing need for improvement is important especially at species level.
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Grégory D, Chaudet H, Lagier JC, Raoult D. How mass spectrometric approaches applied to bacterial identification have revolutionized the study of human gut microbiota. Expert Rev Proteomics 2018; 15:217-229. [PMID: 29336192 DOI: 10.1080/14789450.2018.1429271] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions. Areas covered: This review first underlines how mass spectrometric approaches have revolutionized clinical microbiology. It then highlights the contribution of MS-based methods to culturomics studies, paying particular attention to the extension of the human gut microbiota repertoire through the discovery of new bacterial species. Expert commentary: MS-based approaches have enabled cultivation methods to be resuscitated to study the human gut microbiota and thus to fill in the blanks left by high-throughput sequencing methods in terms of culturing minority populations. Continued efforts to recover new taxa using culture methods, combined with their rapid implementation in genomic databases, would allow for an exhaustive analysis of the gut microbiota through the use of a comprehensive approach.
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Affiliation(s)
- Dubourg Grégory
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Hervé Chaudet
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Jean-Christophe Lagier
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
| | - Didier Raoult
- a Aix Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), Assistance Publique - Hôpitaux de Marseille - IHU Méditerranée Infection , Marseille , France
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Kee SJ, Suh SP. Increasing Burden of Nontuberculous Mycobacteria in Korea. J Korean Med Sci 2017; 32:1215-1216. [PMID: 28665053 PMCID: PMC5494316 DOI: 10.3346/jkms.2017.32.8.1215] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 11/20/2022] Open
Affiliation(s)
- Seung Jung Kee
- Department of Laboratory Medicine, Chonnam National University Medical School and Hospital, Gwangju, Korea
| | - Soon Pal Suh
- Department of Laboratory Medicine, Chonnam National University Medical School and Hospital, Gwangju, Korea.
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Evaluation of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Identification of Mycobacterium abscessus Subspecies According to Whole-Genome Sequencing. J Clin Microbiol 2016; 54:2982-2989. [PMID: 27682129 DOI: 10.1128/jcm.01151-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/19/2016] [Indexed: 12/22/2022] Open
Abstract
This study was undertaken to evaluate the utility of matrix-assisted laser desorption ionization-time of flight mass spectrometry with the Vitek MS Plus system for identifying Mycobacterium abscessus subspecies in order to facilitate more rapid and appropriate therapy. A total of 175 clinical M. abscessus strains were identified by whole-genome sequencing analysis: 139 Mycobacterium abscessus subsp. abscessus and 36 Mycobacterium abscessus subsp. massiliense The research-use-only (RUO) Saramis Knowledge Base database v.4.12 was modified accordingly by adding 40 M. abscessus subsp. abscessus and 19 M. abscessus subsp. massiliense reference spectra to construct subspecies SuperSpectra. A blind test, used to validate the remaining 116 isolates, yielded 99.1% (n = 115) reliability and only 0.9% (n = 1) error for subspecies identification. Among the two subspecies SuperSpectra, two specific peaks were found for M. abscessus subsp. abscessus and four specific peaks were found for M. abscessus subsp. massiliense Our study is the first to report differential peaks 3,354.4 m/z and 6,711.1 m/z, which were specific for M. abscessus subsp. massiliense Our research demonstrates the capacity of the Vitek MS RUO Saramis Knowledge Base database to identify M. abscessus at the subspecies level. Moreover, it validates the potential ease and accuracy with which it can be incorporated into the IVD system for the identification of M. abscessus subspecies.
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Abstract
ABSTRACT
The immunocompromised host is at increased risk of
Mycobacterium tuberculosis
complex and nontuberculous mycobacteria infection. Although
Mycobacterium tuberculosis
complex is a significant mycobacterial pathogen, nontuberculous mycobacteria causes substantial disease in those with suppressed immune responses. Mycobacterial infections can cause significant morbidity and mortality in this patient population, and rapid identification and susceptibility testing of the mycobacterial species is paramount to patient management and outcomes. Mycobacterial diagnostics has undergone some significant advances in the last two decades with immunodiagnostics (interferon gamma release assay), microscopy (light-emitting diode), culture (automated broth-based systems), identification (direct PCR, sequencing and matrix-assisted laser-desorption ionization–time of flight mass spectrometry) and susceptibility testing (molecular detection of drug resistance from direct specimens or positive cultures). Employing the most rapid and sensitive methods in the mycobacterial laboratory will have a tremendous impact on patient care and, in the case of
Mycobacterium tuberculosis
complex, in the control of tuberculosis.
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Lee MR, Tsai CJ, Hu JY, Lee SW, Ko JC, Wang HC, Yu CJ, Lee LN, Hsueh PR. Acquisition of Mycobacterium abscessus among ventilator-dependent patients in Taiwan chronic respiratory care facilities. Future Microbiol 2016; 11:491-500. [PMID: 27064349 DOI: 10.2217/fmb.16.6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To investigate the acquisition of Mycobacterium abscessus among ventilator-dependent patients. MATERIALS & METHODS We prospectively recruited ventilator-dependent patients in five respiratory care wards (RCWs). Respiratory specimens were cultured for mycobacteria on day 1 (D1), 3 months (M3) and 6 months (M6) after enrollment. RESULTS 72 patients had cultures taken at all three time points. The proportion of patients with a culture positive for M. abscessus increased from 15.3% (11/72) on D1 to 30.6% (22/72) at M3 and 38.9% (28/72) at M6. Two M. abscessus subspecies abscessus isolates obtained from different patients had identical randomly amplified polymorphic DNA patterns. Being in RCW D and advanced age were significantly associated with initial cultures positivity. CONCLUSION Our study reveals that acquisition of M. abscessus was common among ventilator-dependent patients.
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Affiliation(s)
- Meng-Rui Lee
- Department of Internal Medicine, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.,Institute of Preventive Epidemiology & Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health & Welfare, Taoyuan City, Taiwan
| | - Chia-Jung Tsai
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health & Welfare, Taoyuan City, Taiwan
| | - Jia-Ying Hu
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health & Welfare, Taoyuan City, Taiwan
| | - Shih-Wei Lee
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health & Welfare, Taoyuan City, Taiwan
| | - Jen-Chung Ko
- Department of Internal Medicine, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan
| | - Hao-Chien Wang
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chong-Jen Yu
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Li-Na Lee
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University College of Medicine, National Taiwan University Hospital, Taipei, Taiwan
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13
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Suzuki H, Yoshida S, Yoshida A, Okuzumi K, Fukusima A, Hishinuma A. A novel cluster of Mycobacterium abscessus complex revealed by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS). Diagn Microbiol Infect Dis 2015; 83:365-70. [DOI: 10.1016/j.diagmicrobio.2015.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/16/2015] [Accepted: 08/21/2015] [Indexed: 10/23/2022]
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14
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Hoshino Y, Suzuki K. Differential diagnostic assays for discriminating mycobacteria, especially for nontuberculous mycobacteria: what does the future hold? Future Microbiol 2015; 10:205-16. [PMID: 25689533 DOI: 10.2217/fmb.14.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Mycobacteria infections are an important medical problem, and many are regarded as emerging and re-emerging diseases. Mycobacterium tuberculosis, the causative agent of tuberculosis, remains a leading cause of human morbidity and mortality worldwide, with approximately 8.6 million cases and 1.3 million deaths in 2012. In addition, the incidence of nontuberculous Mycobacterium infection has significantly increased, especially among developed countries. Although phenotypical appearances such as culture characteristics and/or susceptibility to anti-Mycobacterium drugs are variable between different mycobacterial species, early diagnosis is crucial in terms of patient treatment and clinical outcome. In this manuscript, we describe the development of diagnostic techniques, from the classical/conventional to the most recent advances, and provide an overview of the future direction of discrimination procedures.
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Affiliation(s)
- Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba, Higashi-Murayama, Tokyo, Japan
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15
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O'Connor JA, O'Reilly B, Corcoran GD, O'Mahony J, Lucey B. Mycobacterium diagnostics: from the primitive to the promising. Br J Biomed Sci 2015; 72:32-41. [PMID: 25906489 DOI: 10.1080/09674845.2015.11666793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The field of clinical microbiology has been revolutionised by genomic and proteomic methods, which have facilitated more rapid diagnosis and characterisation of infection in many cases. In contrast, mycobacteriological evolution has tended to retain the traditional methods of smear microscopy for detection of acid-fast bacilli to indicate mycobacteria, along with culture, and in synergy with more modern molecular methods. Thus, efforts have been focused on reducing the time to diagnosis of infection, while increasing the amount of diagnostic information available, including more definitive speciation, and more rapid susceptibility test results. Although smear microscopy remains a mainstay for the laboratory-based diagnosis of mycobacterial infection, molecular testing has vastly reduced the time needed for identification of Mycobacterium tuberculosis in particular, when compared with traditional culture-based techniques. Molecular methods may also yield antimicrobial susceptibility results through testing for the most common resistance-inducing mutations to some of the antimicrobial agents of choice. However, the diversity of resistance mutations already characterised suggests that these currently-available molecular detection systems should be accompanied by culture-based susceptibility testing. This review compares the efficacy of microscopic, phenotypic, proteomic and genotypic methods available for mycobacterial diagnosis. The diversity of methods currently in use reflects the complexity of this area of diagnostic microbiology.
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