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Dinh-Hung N, Mwamburi SM, Dong HT, Rodkhum C, Meemetta W, Linh NV, Mai HN, Dhar AK, Hirono I, Senapin S, Chatchaiphan S. Unveiling Insights into the Whole Genome Sequencing of Mycobacterium spp. Isolated from Siamese Fighting Fish ( Betta splendens). Animals (Basel) 2024; 14:2833. [PMID: 39409782 PMCID: PMC11476334 DOI: 10.3390/ani14192833] [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: 07/26/2024] [Revised: 09/18/2024] [Accepted: 09/29/2024] [Indexed: 10/20/2024] Open
Abstract
This study aims to genomically elucidate six isolates of rapidly growing non-tuberculous mycobacteria (RGM) derived from Siamese fighting fish (Betta splendens). These isolates had previously undergone phenotypic and biochemical characterization, antibiotic susceptibility testing, and in vivo virulence assessment. Initial DNA barcoding using the 16S rRNA sequence assigned these six isolates to five different species, namely Mycobacterium chelonae (BN1983), M. cosmeticum (BN1984 and N041), M. farcinogenes (SNSK5), M. mucogenicum (BN1956), and M. senegalense (BN1985). However, the identification relied solely on the highest percent identity of the 16S rRNA gene, raising concerns about the taxonomic ambiguity of these species. Comprehensive whole genome sequencing (WGS) and extended genomic comparisons using multilocus sequence typing (MLST), average nucleotide identity (ANI), and digital DNA-DNA hybridization (dDDH) led to the reclassification of BN1985 and SNSK5 as M. conceptionense while confirming BN1983 as M. chelonae and BN1984 and N041 as M. cosmeticum. Notably, the analysis of the BN1956 isolate revealed a potential new species that is proposed here as M. mucogenicum subsp. phocaicum sp. nov. Common genes encoding "mycobacterial" virulence proteins, such as PE and PPE family proteins, MCE, and YrbE proteins, were detected in all six isolates. Two species, namely M. chelonae and M. cosmeticum, appear to have horizontally acquired T6SS-II (clpB), catalase (katA), GroEL (groel), and capsule (rmlb) from distantly related environmental bacteria such as Klebsiella sp., Neisseria sp., Clostridium sp., and Streptococcus sp. This study provides the first draft genome sequence of RGM isolates currently circulating in B. splendens and underscores the necessity of WGS for the identification and classification of mycobacterial species.
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Affiliation(s)
- Nguyen Dinh-Hung
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721, USA; (N.D.-H.); (H.N.M.); (A.K.D.)
| | - Samuel Mwakisha Mwamburi
- Kenya Marine and Fisheries Research Institute, Mombasa 80100, Kenya;
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan;
| | - Ha Thanh Dong
- Aquaculture and Aquatic Resources Management (AARM), School of Environment, Resources and Development, Asian Institute of Technology (AIT), Pathum Thani 12120, Thailand;
| | - Channarong Rodkhum
- Center of Excellence in Fish Infectious Diseases (CE FID), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Watcharachai Meemetta
- Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Nguyen Vu Linh
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
| | - Hung N. Mai
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721, USA; (N.D.-H.); (H.N.M.); (A.K.D.)
| | - Arun K. Dhar
- Aquaculture Pathology Laboratory, School of Animal & Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ 85721, USA; (N.D.-H.); (H.N.M.); (A.K.D.)
| | - Ikuo Hirono
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan;
| | - Saengchan Senapin
- Fish Health Platform, Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Satid Chatchaiphan
- Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
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Zhao A, Li Y, Wu L, Wang Z, Lv Y, Xiong W, Alam MA, Liu G, Xu J. Immobilization of rough morphotype Mycolicibacterium neoaurum R for androstadienedione production. Biotechnol Lett 2024; 46:55-68. [PMID: 38064040 DOI: 10.1007/s10529-023-03448-x] [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: 05/28/2023] [Revised: 09/20/2023] [Accepted: 11/04/2023] [Indexed: 01/14/2024]
Abstract
OBJECTIVES Enhance the androstadienedione (Androst-1,4-diene-3,17-dione, ADD) production of rough morphotype Mycolicibacterium neoaurum R by repeated-batch fermentation of immobilized cells. RESULTS M. neoaurum R was a rough colony morphotype variant, obtained from the routine plating of smooth M. neoaurum strain CICC 21097. M. neoaurum R showed rougher cell surface and aggregated in broth. The ADD production of M. neoaurum R was notably lower than that of M. neoaurum CICC 21097 during the free cell fermentation, but the yield gap could be erased after proper cell immobilization. Subsequently, repeated-batch fermentation of immobilized M. neoaurum R was performed to shorten the production cycle and enhance the bio-production efficiency of ADD. Through the optimization of the immobilization carriers and the co-solvents for phytosterols, the ADD productivity of M. neoaurum R immobilized by semi-expanded perlite reached 0.075 g/L/h during the repeated-batch fermentation for 40 days. CONCLUSIONS The ADD production of the rough-type M. neoaurum R was notably enhanced by the immobilization onto semi-expanded perlite. Moreover, the ADD batch yields of M. neoaurum R immobilized by semi-expanded perlite were maintained at high levels during the repeated-batch fermentation.
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Affiliation(s)
- Anqi Zhao
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yamei Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Lixia Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zhi Wang
- School of Chemical Engineering, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yongkun Lv
- School of Chemical Engineering, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Wenlong Xiong
- School of Chemical Engineering, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Mohammad Asraful Alam
- School of Chemical Engineering, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Guohua Liu
- Key Laboratory of Feed Biotechnology, The Ministry of Agriculture and Rural Affairs of the People's Republic of China, Beijing, 100081, China
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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Yang J, Hu Y, Zhang Y, Zhou S, Meng D, Xia S, Wang H. Deciphering the diversity and assemblage mechanisms of nontuberculous mycobacteria community in four drinking water distribution systems with different disinfectants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 907:168176. [PMID: 37907107 DOI: 10.1016/j.scitotenv.2023.168176] [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: 09/04/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/02/2023]
Abstract
Nontuberculous mycobacteria (NTM) represent an emerging health concern due to their escalating infections worldwide. Although drinking water distribution systems (DWDSs) have been considered as NTM reservoirs and a potential infection route, NTM community at the species level remain largely elusive in DWDSs. This study employed high-throughput sequencing coupled with qPCR to profile NTM community and estimate their abundances at the species level in water and biofilm samples in four DWDSs using three different disinfectants (i.e. free chlorine, chloramine and chlorine dioxide). Results demonstrated the dominance of Mycobacterium paragordonae and Mycobacterium mucogenicum in both biofilm and water across four DWDSs, whereas Mycobacterium abscessus and Mycobacterium chelonae, the two clinically significant species, exhibited low abundance but high prevalence. Comparable NTM community was observed in biofilm across these four DWDSs. Distinct separation of NTM community between SH-chloramine DWDSs water and other DWDSs highlighted the selective pressure of chloramine on NTM community. Furthermore, the research revealed that biofilm and water exhibited distinct NTM community structures, with biofilm harboring more diverse NTM community. Certain NTM species displayed a preference for biofilm, such as Mycobacterium gordonae, while others, like Mycobacterium mucogenicum, were more abundant in water samples (P < 0.05). In terms of NTM community assembly, stochastic processes dominated biofilm, while comparable role of stochastic and deterministic processes was observed in water. In conclusion, this study offers a pioneering and comprehensive insight into the dynamics and assembly mechanisms of NTM community within four DWDSs treated with three distinct disinfectants. These findings serve as a critical foundation for assessing NTM exposure risks and devising effective management strategies within DWDSs.
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Affiliation(s)
- Jinhao Yang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yuxing Hu
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yue Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Shuang Zhou
- School of Medicine, Tongji University, Shanghai 200092, China
| | - Die Meng
- Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Hong Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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Mohebbipour‐Loren A, Soghrati M, Barin S, Rezaei M. A case report of cutaneous infection with Mycobacterium neoaurum. Clin Case Rep 2023; 11:e7265. [PMID: 37143460 PMCID: PMC10151593 DOI: 10.1002/ccr3.7265] [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: 11/24/2022] [Revised: 03/21/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023] Open
Abstract
Cutaneous infection due to Mycobacterium neoaurum in immune-competent individuals had only been reported in limited cases. The point that makes our case very impressive was its cutaneous infection, and presentation in the immune-competent patient. Abstract Cutaneous infections caused by nontuberculous mycobacteria usually occur in immunocompromised hosts. We report a rare case of cutaneous infection caused by Mycobacterium neoaurum in an immune-competent patient.
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Affiliation(s)
| | | | - Sajjad Barin
- Pathology Department, School of MedicineArdabil University of Medical SciencesArdabilIran
| | - Mitra Rezaei
- Pathology Department, School of MedicineShahid Beheshti University of Medical SciencesTehranIran
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Behra PRK, Pettersson BMF, Ramesh M, Das S, Dasgupta S, Kirsebom LA. Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA. BMC Genomics 2022; 23:704. [PMID: 36243697 PMCID: PMC9569102 DOI: 10.1186/s12864-022-08927-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Mycobacterium genus encompasses at least 192 named species, many of which cause severe diseases such as tuberculosis. Non-tuberculosis mycobacteria (NTM) can also infect humans and animals. Some are of emerging concern because they show high resistance to commonly used antibiotics while others are used and evaluated in bioremediation or included in anticancer vaccines. RESULTS We provide the genome sequences for 114 mycobacterial type strains and together with 130 available mycobacterial genomes we generated a phylogenetic tree based on 387 core genes and supported by average nucleotide identity (ANI) data. The 244 genome sequences cover most of the species constituting the Mycobacterium genus. The genome sizes ranged from 3.2 to 8.1 Mb with an average of 5.7 Mb, and we identified 14 new plasmids. Moreover, mycobacterial genomes consisted of phage-like sequences ranging between 0 and 4.64% dependent on mycobacteria while the number of IS elements varied between 1 and 290. Our data also revealed that, depending on the mycobacteria, the number of tRNA and non-coding (nc) RNA genes differ and that their positions on the chromosome varied. We identified a conserved core set of 12 ncRNAs, 43 tRNAs and 18 aminoacyl-tRNA synthetases among mycobacteria. CONCLUSIONS Phages, IS elements, tRNA and ncRNAs appear to have contributed to the evolution of the Mycobacterium genus where several tRNA and ncRNA genes have been horizontally transferred. On the basis of our phylogenetic analysis, we identified several isolates of unnamed species as new mycobacterial species or strains of known mycobacteria. The predicted number of coding sequences correlates with genome size while the number of tRNA, rRNA and ncRNA genes does not. Together these findings expand our insight into the evolution of the Mycobacterium genus and as such they establish a platform to understand mycobacterial pathogenicity, their evolution, antibiotic resistance/tolerance as well as the function and evolution of ncRNA among mycobacteria.
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Affiliation(s)
- Phani Rama Krishna Behra
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - B. M. Fredrik Pettersson
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Malavika Ramesh
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Sarbashis Das
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
| | - Leif A. Kirsebom
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Box 596, SE-751 24 Uppsala, Sweden
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Wang XX, Ke X, Liu ZQ, Zheng YG. Rational development of mycobacteria cell factory for advancing the steroid biomanufacturing. World J Microbiol Biotechnol 2022; 38:191. [PMID: 35974205 PMCID: PMC9381402 DOI: 10.1007/s11274-022-03369-3] [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: 06/23/2022] [Accepted: 07/28/2022] [Indexed: 12/05/2022]
Abstract
Steroidal resource occupies a vital proportion in the pharmaceutical industry attributing to their important therapeutic effects on fertility, anti-inflammatory and antiviral activities. Currently, microbial transformation from phytosterol has become the dominant strategy of steroidal drug intermediate synthesis that bypasses the traditional chemical route. Mycobacterium sp. serve as the main industrial microbial strains that are capable of introducing selective functional modifications of steroidal intermediate, which has become an indispensable platform for steroid biomanufacturing. By reviewing the progress in past two decades, the present paper concentrates mainly on the microbial rational modification aspects that include metabolic pathway editing, key enzymes engineering, material transport pathway reinforcement, toxic metabolic intermediates removal and byproduct reconciliation. In addition, progress on omics analysis and direct genetic manipulation are summarized and classified that may help reform the industrial hosts with more efficiency. The paper provides an insightful present for steroid biomanufacturing especially on the current trends and prospects of mycobacteria.
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Affiliation(s)
- Xin-Xin Wang
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Xia Ke
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Zhi-Qiang Liu
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China. .,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- National and Local Joint Engineering Research Center for Biomanufacturing of Choral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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Shu Q, Rajagopal M, Fan J, Zhan L, Kong X, He Y, Rotcheewaphan S, Lyon CJ, Sha W, Zelazny AM, Hu T. Peptidomic analysis of mycobacterial secreted proteins enables species identification. VIEW 2022. [DOI: 10.1002/viw.20210019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Qingbo Shu
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Meena Rajagopal
- Department of Laboratory Medicine, Clinical Center National Institutes of Health Bethesda Maryland USA
| | - Jia Fan
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Lingpeng Zhan
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Xiangxing Kong
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Yifan He
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital Tongji University School of Medicine Shanghai People's Republic of China
| | - Suwatchareeporn Rotcheewaphan
- Department of Laboratory Medicine, Clinical Center National Institutes of Health Bethesda Maryland USA
- Department of Microbiology, Faculty of Medicine Chulalongkorn University Bangkok Thailand
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
| | - Wei Sha
- Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital Tongji University School of Medicine Shanghai People's Republic of China
| | - Adrian M. Zelazny
- Department of Laboratory Medicine, Clinical Center National Institutes of Health Bethesda Maryland USA
| | - Tony Hu
- Center for Cellular and Molecular Diagnostics Department of Biochemistry and Molecular Biology School of Medicine Tulane University New Orleans Louisiana USA
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Zhao N, Guo J, Zhang B, Liu K, Liu Y, Shen Y, Li J. Heterogeneity of the Tissue-specific Mucosal Microbiome of Normal Grass Carp (Ctenopharyngodon idella). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:366-379. [PMID: 35303209 DOI: 10.1007/s10126-022-10113-3] [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: 12/13/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Microbiome plays key roles in the digestion, metabolism, and immunity of the grass carp (Ctenopharyngodon idella). Here, we characterized the normal microbiome of the intestinal contents (IC), skin mucus (SM), oral mucosa (OM), and gill mucosa (GM) of the grass carp, as well as the microbiome of the sidewall (SW) of the raising pool, using full-length 16S rRNA sequencing based on the PacBio platform in this specie for the first time. Twenty phyla, 38 classes, 130 families, 219 genera, and 291 species were classified. One hundred four common classified species might be core microbiota of grass carp. Proteobacteria, Bacteroides, and Cyanobacteria were the dominant phyla in the niche of grass carp. Proteobacteria and Bacteroides dominated the taxonomic composition in the SM, GM, and OM, while Proteobacteria, Planctomycetota, and Cyanobacteria preponderated in the IC and SW groups. Microbiota of IC exhibited higher alpha diversity indices. The microbial communities clustered either in SW or the niche from grass carp, significantly tighter in the SW, based on Bray-Curtis distances (P < 0.05). SM, GM, and OM were similar in microbial composition but were significantly different from IC and SW, while IC had similarity with SW due to their common Cyanobacteria (P < 0.05). Differences were also reflected by niche-specific and differentially abundant microorganisms such as Noviherbaspirillum in the SM and Rhodopseudomonas palustris, Mycobacterium fortuitum, and Acinetobacter schindleri in GM. Significantly raised gene expression was found in IC and SM associated with cell cycle control, cell division, chromosome, coenzyme transport and metabolism, replication, recombination and repair, cell motility, post-translational modification, signal transduction mechanisms, intracellular trafficking, secretion, and vesicles by PICRUSt. This work may be of great value for understanding of fish-microbial co-workshops, especially in different niche of grass carp.
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Affiliation(s)
- Na Zhao
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Jiamin Guo
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Bo Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, China
| | - Kai Liu
- Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024, China
| | - Yuting Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China
| | - Yubang Shen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
- College of Fisheries and Life Science, Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China.
| | - Jiale Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, Shanghai, 201306, China.
- College of Fisheries and Life Science, Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai, 201306, China.
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Kang M, Kim HW, Yu AR, Yang JS, Lee SH, Lee JW, Yoon HS, Lee BS, Park HW, Lee SK, Lee S, Whang J, Kim JS. Comparison of Macrophage Immune Responses and Metabolic Reprogramming in Smooth and Rough Variant Infections of Mycobacterium mucogenicum. Int J Mol Sci 2022; 23:ijms23052488. [PMID: 35269631 PMCID: PMC8910348 DOI: 10.3390/ijms23052488] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 01/27/2023] Open
Abstract
Mycobacterium mucogenicum (Mmuc), a rapidly growing nontuberculous mycobacterium (NTM), can infect humans (posttraumatic wound infections and catheter-related sepsis). Similar to other NTM species, Mmuc exhibits colony morphologies of rough (Mmuc-R) and smooth (Mmuc-S) types. Although there are several case reports on Mmuc infection, no experimental evidence supports that the R-type is more virulent. In addition, the immune response and metabolic reprogramming of Mmuc have not been studied on the basis of morphological characteristics. Thus, a standard ATCC Mmuc strain and two clinical strains were analyzed, and macrophages were generated from mouse bone marrow. Cytokines and cell death were measured by ELISA and FACS, respectively. Mitochondrial respiration and glycolytic changes were measured by XF seahorse. Higher numbers of intracellular bacteria were found in Mmuc-R-infected macrophages than in Mmuc-S-infected macrophages. Additionally, Mmuc-R induced higher levels of the cytokines TNF-α, IL-6, IL-12p40, and IL-10 and induced more BMDM necrotic death. Furthermore, our metabolic data showed marked glycolytic and respiratory differences between the control and each type of Mmuc infection, and changes in these parameters significantly promoted glucose metabolism, extracellular acidification, and oxygen consumption in BMDMs. In conclusion, at least in the strains we tested, Mmuc-R is more virulent, induces a stronger immune response, and shifts bioenergetic metabolism more extensively than the S-type. This study is the first to report differential immune responses and metabolic reprogramming after Mmuc infection and might provide a fundamental basis for additional studies on Mmuc pathogenesis.
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Affiliation(s)
- Minji Kang
- Department of Medical Science, Chungnam National University, Daejeon 35365, Korea;
| | - Ho Won Kim
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon 35365, Korea; (H.W.K.); (A.-R.Y.); (J.W.L.); (H.S.Y.)
| | - A-Reum Yu
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon 35365, Korea; (H.W.K.); (A.-R.Y.); (J.W.L.); (H.S.Y.)
| | - Jeong Seong Yang
- Korea Mycobacterium Resource Center (KMRC), Department of Research and Development, The Korean Institute of Tuberculosis, Osong 28158, Korea; (J.S.Y.); (S.H.L.)
| | - Seung Heon Lee
- Korea Mycobacterium Resource Center (KMRC), Department of Research and Development, The Korean Institute of Tuberculosis, Osong 28158, Korea; (J.S.Y.); (S.H.L.)
| | - Ji Won Lee
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon 35365, Korea; (H.W.K.); (A.-R.Y.); (J.W.L.); (H.S.Y.)
| | - Hoe Sun Yoon
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon 35365, Korea; (H.W.K.); (A.-R.Y.); (J.W.L.); (H.S.Y.)
| | - Byung Soo Lee
- Department of Ophthalmology, Konyang University Hospital and College of Medicine, Daejeon 35365, Korea;
| | - Hwan-Woo Park
- Department of Cell Biology, Konyang University College of Medicine, Daejeon 35365, Korea;
| | - Sung Ki Lee
- Department of Obstetrics and Gynecology, Konyang University Hospital, Daejeon 35365, Korea;
| | - Seungwan Lee
- Department of Medical Science, Konyang University, 158 Gwanjeodong-ro, Daejeon 35365, Korea;
| | - Jake Whang
- Korea Mycobacterium Resource Center (KMRC), Department of Research and Development, The Korean Institute of Tuberculosis, Osong 28158, Korea; (J.S.Y.); (S.H.L.)
- Correspondence: (J.W.); (J.-S.K.); Tel.: +82-43-249-4974 (J.W.); +82-42-600-8648 (J.-S.K.)
| | - Jong-Seok Kim
- Myunggok Medical Research Institute, College of Medicine, Konyang University, Daejeon 35365, Korea; (H.W.K.); (A.-R.Y.); (J.W.L.); (H.S.Y.)
- Correspondence: (J.W.); (J.-S.K.); Tel.: +82-43-249-4974 (J.W.); +82-42-600-8648 (J.-S.K.)
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Maladan Y, Krismawati H, Wahyuni T, Tanjung R, Awaludin K, Audah KA, Parikesit AA. The whole-genome sequencing in predicting Mycobacterium tuberculosis drug susceptibility and resistance in Papua, Indonesia. BMC Genomics 2021; 22:844. [PMID: 34802420 PMCID: PMC8607662 DOI: 10.1186/s12864-021-08139-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/01/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Tuberculosis is one of the deadliest disease caused by Mycobacterium tuberculosis. Its treatment still becomes a burden for many countries including Indonesia. Drug resistance is one of the problems in TB treatment. However, a development in the molecular field through Whole-genome sequencing (WGS) can be used as a solution in detecting mutations associated with TB- drugs. This investigation intended to implement this data for supporting the scientific community in deeply understanding any TB epidemiology and evolution in Papua along with detecting any mutations in genes associated with TB-Drugs. RESULT A whole-genome sequencing was performed on the random samples from TB Referral Laboratory in Papua utilizing MiSeq 600 cycle Reagent Kit (V3). Furthermore, TBProfiler was used for genome analysis, RAST Server was employed for annotation, while Gview server was applied for BLAST genome mapping and a Microscope server was implemented for Regions of Genomic Plasticity (RGP). The largest genome of M. tuberculosis obtained was at the size of 4,396,040 bp with subsystems number at 309 and the number of coding sequences at 4326. One sample (TB751) contained one RGP. The drug resistance analysis revealed that several mutations associated with TB-drug resistance existed. In details, mutations of rpoB gene which were identified as S450L, D435Y, H445Y, L430P, and Q432K had caused the reduced effectiveness of rifampicin; while the mutases in katG (S315T), kasA (312S), inhA (I21V), and Rv1482c-fabG1 (C-15 T) genes had contributed to the resistance in isoniazid. In streptomycin, the resistance was triggered by the mutations in rpsL (K43R) and rrs (A514C, A514T) genes, and, in Amikacin, its resistance was led by mutations in rrs (A514C) gene. Additionally, in Ethambutol and Pyrazinamide, their reduced effectiveness was provoked by embB gene mutases (M306L, M306V, D1024N) and pncA (W119R). CONCLUSIONS The results from whole-genome sequencing of TB clinical sample in Papua, Indonesia could contribute to the surveillance of TB-drug resistance. In the drug resistance profile, there were 15 Multi Drugs Resistance (MDR) samples. However, Extensively Drug-resistant (XDR) samples have not been found, but samples were resistant to only Amikacin, a second-line drug.
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Affiliation(s)
- Yustinus Maladan
- Center for Papua Health Research and Development, Papua, Indonesia.
| | - Hana Krismawati
- Center for Papua Health Research and Development, Papua, Indonesia
| | - Tri Wahyuni
- Center for Papua Health Research and Development, Papua, Indonesia
| | - Ratna Tanjung
- Center for Papua Health Research and Development, Papua, Indonesia
| | | | | | - Arli Aditya Parikesit
- Department of Bioinformatics, School of Life Sciences, International Institute for Life Sciences (I3L), Jakarta, Indonesia.
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