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Komine T, Fukano H, Yoshida M, Miyamoto Y, Nakaya M, Fujinaga A, Doke K, Hoshino Y. A rapid and simple MALDI-TOF MS lipid profiling method for differentiating Mycobacterium ulcerans from Mycobacterium marinum. J Clin Microbiol 2025; 63:e0140024. [PMID: 39868779 PMCID: PMC11898672 DOI: 10.1128/jcm.01400-24] [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: 09/06/2024] [Accepted: 12/12/2024] [Indexed: 01/28/2025] Open
Abstract
Mycobacterium ulcerans, a slow-growing nontuberculous mycobacterium, causes Buruli ulcer, a neglected tropical disease. Distinguishing M. ulcerans from related species, including Mycobacterium marinum, poses challenges with respect to making accurate identifications. In this study, we developed a rapid and simple identification method based on mycobacterial lipid profiles and used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze the lipid profiles of M. ulcerans (n = 35) and M. marinum (n = 19) isolates. Bacterial colonies pre-cultured on 2% Ogawa egg slants for 2 months were collected, and total lipids were extracted using an MBT Lipid Xtract kit. Spectra were obtained in negative ion mode using a MALDI Biotyper Sirius system, with ClinProTools v3.0 being used to analyze the spectra based on the application of three algorithms (genetic algorithm [GA], supervised neural network [SNN], and quick classifier [QC)]). Cross-validation was performed using a 20% leave-out set randomly selected from the samples. Models generated using GA, SNN, and QC showed cross-validation values of 100%, 100%, and 97.9%, respectively, and all algorithms achieved 100% recognition capability values. Our findings indicate that MALDI-TOF analysis of lipid profiles can accurately differentiate two mycobacterial species (M. ulcerans and M. marinum) that are difficult to distinguish using conventional protein-targeting methods.IMPORTANCEBuruli ulcer, caused by Mycobacterium ulcerans, is a neglected tropical disease. However, distinguishing M. ulcerans from related species, including Mycobacterium marinum, presents certain challenges. In this study, we demonstrate the utility of a rapid yet simple method for differentiating isolates of these mycobacteria based on their lipid profiles using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. This new approach can accurately identify species that are otherwise difficult to distinguish using conventional techniques. This represents a significant diagnostic advance for clinical laboratories, in that it enables a more rapid and precise identification, thereby leading to earlier treatment initiation and more appropriate treatment regimens for infections caused by these bacteria.
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Grants
- JP23fk0108608, JP23fk0108673, JP23gm1610003, JP23gm1610007, JP23wm0125007, JP23wm0225022, JP23wm0325054, JP22fk0108558, JP22fk0108553 Japan Agency for Medical Research and Development (AMED)
- JP22fk0108573, JP23wm0225022 Japan Agency for Medical Research and Development (AMED)
- JP23wm0325054, JP22fk0108558, JP22fk0108553 Japan Agency for Medical Research and Development (AMED)
- JP22K16382 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP24K19189 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP63KK0138-A, JP23K07665 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP63KK0138-B, JP23K07958 MEXT | Japan Society for the Promotion of Science (JSPS)
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Affiliation(s)
- Takeshi Komine
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Hanako Fukano
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Mitsunori Yoshida
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Yuji Miyamoto
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Makoto Nakaya
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Azumi Fujinaga
- Application Department, Microbiology & Diagnostics MID Division, Bruker Japan K.K., Yokohama, Kanagawa, Japan
| | - Kohei Doke
- Application Department, Microbiology & Diagnostics MID Division, Bruker Japan K.K., Yokohama, Kanagawa, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
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Wada T, Yoshida S, Yamamoto T, Nonaka L, Fukushima Y, Nakajima C, Suzuki Y, Imajoh M. Application of Genomic Epidemiology of Pathogens to Farmed Yellowtail Fish Mycobacteriosis in Kyushu, Japan. Microbes Environ 2024; 39:ME24011. [PMID: 38897967 PMCID: PMC11220446 DOI: 10.1264/jsme2.me24011] [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: 02/15/2024] [Accepted: 05/15/2024] [Indexed: 06/21/2024] Open
Abstract
To investigate mycobacterial cases of farmed yellowtail fish in coastal areas of western Japan (Kagoshima, Kyushu), where aquaculture fisheries are active, Mycobacterium pseudoshottsii, the causative agent, was isolated from six neighboring fishing ports in 2012 and 2013. A phylogenetic ana-lysis revealed that the strains isolated from one fishing port were closely related to those isolated from other regions of Japan, suggesting the nationwide spread of a single strain. However, strains from Japan were phylogenetically distinct from those from the Mediterranean and the United States; therefore, worldwide transmission was not observed based on the limited data obtained on the strains exami-ned in this study. The present results demonstrate that a bacterial genomic ana-lysis of infected cases, a mole-cular epidemiology strategy for public health, provides useful data for estimating the prevalence and transmission pathways of M. pseudoshottsii in farmed fish. A bacterial genome ana-lysis of strains, such as that performed herein, may play an important role in monitoring the prevalence of this pathogen in fish farms and possible epidemics in the future as a result of international traffic, logistics, and trade in fisheries.
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Affiliation(s)
- Takayuki Wada
- Department of Microbiology, Graduate School of Human Life and Ecology, Osaka Metropolitan University, Osaka, Japan
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Sakai, Osaka, Japan
| | - Takeshi Yamamoto
- Azuma-cho Fisheries Cooperative Association, Izumi, Kagoshima, Japan
| | - Lisa Nonaka
- Faculty of Human Life Sciences, Shokei University, Kumamoto, Kumamoto, Japan
| | - Yukari Fukushima
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Chie Nakajima
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Division of Research Support, Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- Division of Research Support, Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Masayuki Imajoh
- Laboratory of Fish Disease, Aquaculture Course, Department of Marine Resource Science, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
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Imajoh M, Yoshida S, Nonaka L, Fukushima Y, Nakajima C, Suzuki Y, Wada T. Retrospective identification of pathogenic mycobacterial species in fish: Mycobacterium pseudoshottsii YM-3, isolated from a yellowtail fish in 1986 in Kochi, Japan. Microbiol Resour Announc 2023; 12:e0049823. [PMID: 37712690 PMCID: PMC10586100 DOI: 10.1128/mra.00498-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/03/2023] [Indexed: 09/16/2023] Open
Abstract
The complete genome sequence of mycobacterial strain YM-3, isolated from cultured yellowtail in 1986, was determined. The strain was Mycobacterium pseudoshottsii, a closely related subspecies of Mycobacterium marinum, so the strain was isolated earlier than the first report of the subspecies in 2005.
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Affiliation(s)
- Masayuki Imajoh
- Department of Marine Resource Science, Laboratory of Fish Disease, Aquaculture Course, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Sakai, Osaka, Japan
| | - Lisa Nonaka
- Faculty of Human Life Sciences, Shokei University, Kumamoto, Kumamoto, Japan
| | - Yukari Fukushima
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Chie Nakajima
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Research Support, Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Research Support, Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Takayuki Wada
- Department of Microbiology, Graduate School of Human Life and Ecology, Osaka Metropolitan University, Osaka, Japan
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
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Complete Genome and Partial Megaplasmid Sequences of Mycobacterium pseudoshottsii Strain NJB1907-Z4, Isolated from an Aquarium-Reared Japanese Sardine (Sardinops melanostictus) in Japan. Microbiol Resour Announc 2022; 11:e0078522. [DOI: 10.1128/mra.00785-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Mycobacterium pseudoshottsii
, a slow-growing nontuberculous mycobacterium, has been isolated from wild and cultured fish. We report here the complete genome and partial megaplasmid sequences of a strain isolated from an aquarium-reared Japanese sardine (
Sardinops melanostictus
) in Japan,
M. pseudoshottsii
NJB1907-Z4.
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