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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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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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Igarashi Y, Chikamatsu K, Sano S, Miyamoto S, Aono A, Osugi A, Morishige Y, Murase Y, Yamada H, Takaki A, Mitarai S. Development of a nucleic acid chromatography assay for the detection of commonly isolated rapidly growing mycobacteria. J Med Microbiol 2021; 70. [PMID: 34878370 DOI: 10.1099/jmm.0.001464] [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: 11/18/2022] Open
Abstract
Introduction. Non-tuberculosis mycobacterium infections are increasing worldwide, including those caused by rapidly growing mycobacteria (RGM).Gap Statement. The identification of the aetiological agent in the context of infections is essential for the adoption of an adequate therapeutic approach. However, the methods for the rapid distinction of different RGM species are less than optimal.Aim. To develop a nucleic acid chromatography kit to identify clinically common RGM.Methodology. We tried to develop a nucleic acid chromatography kit designed to detect four RGM species (including three subspecies) i.e. Mycobacterium abscessus subsp. abscessus, Mycobacterium abscessus subsp. bolletii (detected as M. abscessus/bolletii) Mycobacterium abscessus subsp. massiliense, Mycobacterium fortuitum, Mycobacterium chelonae and Mycobacterium peregrinum. The amplified target genes for each species/subspecies using multiplex PCR were analysed using a nucleic acid chromatography assay.Results. Among the 159 mycobacterial type strains and 70 RGM clinical isolates tested, the developed assay correctly identified all relevant RGM without any cross-reactivity or false-negatives. The limits of detection for each species were approximately 0.2 pg µl-1.Conclusion. The rapid and simple nucleic acid chromatography method developed here, which does not involve heat denaturation, may contribute to the rapid identification and treatment of RGM infections.
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Affiliation(s)
- Yuriko Igarashi
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA), 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Kinuyo Chikamatsu
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA), 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Sotaro Sano
- Medical SV, Kaneka Corporation, 1-8 Miyamaemachi, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Shigehiko Miyamoto
- Medical SV, Kaneka Corporation, 1-8 Miyamaemachi, Takasago-cho, Takasago, Hyogo 676-8688, Japan
| | - Akio Aono
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA), 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Asami Osugi
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA), 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Yuta Morishige
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA), 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Yoshiro Murase
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA), 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA), 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Akiko Takaki
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA), 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA), 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan.,Department of Basic Mycobacteriology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
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Mase A, Yamaguchi F, Funaki T, Yamazaki Y, Shikama Y, Fukuchi K. PCR amplification of the erm(41) gene can be used to predict the sensitivity of Mycobacterium abscessus complex strains to clarithromycin. Exp Ther Med 2019; 19:945-955. [PMID: 32010256 PMCID: PMC6966227 DOI: 10.3892/etm.2019.8289] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 05/08/2019] [Indexed: 11/06/2022] Open
Abstract
A worldwide increase in the Mycobacterium abscessus (M. abscessus) complex has been observed. Therefore, the aim of the present study was to investigate the diversity of the rrl and erm(41) genes, both of which are associated with macrolide sensitivity in the M. abscessus complex. The current study also examined the efficacy of mass spectrometry as an alternative to molecular testing to classify subspecies of the M. abscessus complex. A total of 14 strains of the M. abscessus complex were obtained, and based on conventional analyses using housekeeping genes, 57% were determined to be M. abscessus subsp. abscessus, 43% were M. abscessus subsp. massiliense, and none were identified as M. abscessus subsp. bolletii. However, depending on the strain, it was not always possible to distinguish between the subspecies by mass spectrometry. Consequently, PCR products for the rrl and erm(41) genes were directly sequenced. Overall, 7.1% of the strains were identified to have a rrl mutation, and 92.9% carried a T at position 28 of erm(41). Results presented here suggest that the principal cause of treatment failure for M. abscessus complex infections is inducible macrolide resistance encoded by the erm(41) gene. From a strictly pragmatic standpoint, the phenotypic function of a putative erm(41) gene is the most important piece of information required by clinicians in order to prescribe an effective treatment. Although PCR amplification of erm(41) is not sufficient to differentiate between the M. abscessus complex subspecies, PCR can be easily and efficiently used to predict the sensitivity of members of the M. abscessus complex to clarithromycin.
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Affiliation(s)
- Ayaka Mase
- Department of Clinical Pathology, Showa University School of Medicine, Tokyo 142-8666, Japan.,Department of Respiratory Medicine, Showa University Fujigaoka Hospital, Yokohama, Kanagawa 227-8501, Japan
| | - Fumihiro Yamaguchi
- Department of Clinical Pathology, Showa University School of Medicine, Tokyo 142-8666, Japan.,Department of Respiratory Medicine, Showa University Fujigaoka Hospital, Yokohama, Kanagawa 227-8501, Japan
| | - Toshitaka Funaki
- Department of Respiratory Medicine, Showa University Fujigaoka Hospital, Yokohama, Kanagawa 227-8501, Japan
| | - Yohei Yamazaki
- Department of Respiratory Medicine, Showa University Fujigaoka Hospital, Yokohama, Kanagawa 227-8501, Japan
| | - Yusuke Shikama
- Department of Respiratory Medicine, Showa University Fujigaoka Hospital, Yokohama, Kanagawa 227-8501, Japan
| | - Kunihiko Fukuchi
- Department of Clinical Pathology, Showa University School of Medicine, Tokyo 142-8666, Japan
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Jones RS, Shier KL, Master RN, Bao JR, Clark RB. Current significance of the Mycobacterium chelonae-abscessus group. Diagn Microbiol Infect Dis 2019; 94:248-254. [PMID: 30954313 DOI: 10.1016/j.diagmicrobio.2019.01.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 02/08/2023]
Abstract
Organisms of the Mycobacterium chelonae-abscessus group can be significant pathogens in humans. They produce a number of diseases including acute, invasive and chronic infections, which may be difficult to diagnose correctly. Identification among members of this group is complicated by differentiating at least eleven (11) known species and subspecies and complexity of identification methodologies. Treatment of their infections may be problematic due to their correct species identification, antibiotic resistance, their differential susceptibility to the limited number of drugs available, and scarcity of susceptibility testing.
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Affiliation(s)
- Robert S Jones
- Infectious Disease Department, Quest Diagnostics Nichols Institute, Chantilly, VA 20131
| | - Kileen L Shier
- Infectious Disease Department, Quest Diagnostics Nichols Institute, Chantilly, VA 20131
| | - Ronald N Master
- Infectious Disease Department, Quest Diagnostics Nichols Institute, Chantilly, VA 20131
| | - Jian R Bao
- Infectious Disease Department, Quest Diagnostics Nichols Institute, Chantilly, VA 20131
| | - Richard B Clark
- Infectious Disease Department, Quest Diagnostics Nichols Institute, Chantilly, VA 20131.
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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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Sabin AP, Ferrieri P, Kline S. Mycobacterium abscessus Complex Infections in Children: A Review. Curr Infect Dis Rep 2017; 19:46. [PMID: 28983867 PMCID: PMC5821427 DOI: 10.1007/s11908-017-0597-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW Infections in children with Mycobacterium abscessus complex represent a particular challenge for clinicians. Increasing incidence of these infections worldwide has necessitated focused attention to improve both diagnostic as well as treatment modalities. Published medical literature was reviewed, with emphasis on material published in the past 5 years. RECENT FINDINGS Increasing availability of new diagnostic tools, such as matrix-assisted laser desorption ionization-time of flight mass spectrometry and custom PCRs, has provided unique insights into the subspecies within the complex and improved diagnostic certainty. Microbiological review of all recent isolates at the University of Minnesota Medical Center was also conducted, with description of the antimicrobial sensitivity patterns encountered in our center, and compared with those published from other centers in the recent literature. A discussion of conventional antimicrobial treatment regimens, alongside detailed description of the relevant antimicrobials, is derived from recent publications. Antimicrobial therapy, combined with surgical intervention in some cases, remains the mainstay of pediatric care. Ongoing questions remain regarding the transmission mechanics, immunologic vulnerabilities exploited by these organisms in the host, and the optimal antimicrobial regimens necessary to enable a reliable cure. Updated treatment guidelines based on focused clinical studies in children and accounting especially for the immunocompromised children at greatest risk are very much needed.
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Affiliation(s)
- Arick P Sabin
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota Medical School, 420 Delaware Street SE, MMC # 250, Minneapolis, MN, 55455, USA
| | - Patricia Ferrieri
- Department of Laboratory Medicine and Pathology and Department of Pediatrics, Division of Infectious Diseases, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Susan Kline
- Department of Medicine, Division of Infectious Diseases and International Medicine, University of Minnesota Medical School, 420 Delaware Street SE, MMC # 250, Minneapolis, MN, 55455, USA.
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Pranada AB, Witt E, Bienia M, Kostrzewa M, Timke M. Accurate differentiation of Mycobacterium chimaera from Mycobacterium intracellulare by MALDI-TOF MS analysis. J Med Microbiol 2017; 66:670-677. [DOI: 10.1099/jmm.0.000469] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Arthur B Pranada
- MVZ Dr. Eberhard & Partner Dortmund (ÜBAG), Department of Medical Microbiology, Dortmund, Germany
| | - Ellen Witt
- MVZ Dr. Eberhard & Partner Dortmund (ÜBAG), Department of Medical Microbiology, Dortmund, Germany
| | - Michael Bienia
- MVZ Dr. Eberhard & Partner Dortmund (ÜBAG), Department of Medical Microbiology, Dortmund, Germany
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The Technical and Biological Reproducibility of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Based Typing: Employment of Bioinformatics in a Multicenter Study. PLoS One 2016; 11:e0164260. [PMID: 27798637 PMCID: PMC5087883 DOI: 10.1371/journal.pone.0164260] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/22/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The technical, biological, and inter-center reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS) typing data has not yet been explored. The aim of this study is to compare typing data from multiple centers employing bioinformatics using bacterial strains from two past outbreaks and non-related strains. MATERIAL/METHODS Participants received twelve extended spectrum betalactamase-producing E. coli isolates and followed the same standard operating procedure (SOP) including a full-protein extraction protocol. All laboratories provided visually read spectra via flexAnalysis (Bruker, Germany). Raw data from each laboratory allowed calculating the technical and biological reproducibility between centers using BioNumerics (Applied Maths NV, Belgium). RESULTS Technical and biological reproducibility ranged between 96.8-99.4% and 47.6-94.4%, respectively. The inter-center reproducibility showed a comparable clustering among identical isolates. Principal component analysis indicated a higher tendency to cluster within the same center. Therefore, we used a discriminant analysis, which completely separated the clusters. Next, we defined a reference center and performed a statistical analysis to identify specific peaks to identify the outbreak clusters. Finally, we used a classifier algorithm and a linear support vector machine on the determined peaks as classifier. A validation showed that within the set of the reference center, the identification of the cluster was 100% correct with a large contrast between the score with the correct cluster and the next best scoring cluster. CONCLUSIONS Based on the sufficient technical and biological reproducibility of MALDI-TOF MS based spectra, detection of specific clusters is possible from spectra obtained from different centers. However, we believe that a shared SOP and a bioinformatics approach are required to make the analysis robust and reliable.
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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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