1
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Sarhan MS, Wurst C, Tzankov A, Bircher AJ, Wittig H, Briellmann T, Augsburger M, Hotz G, Zink A, Maixner F. A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland. BMC Biol 2023; 21:9. [PMID: 36747166 PMCID: PMC9903526 DOI: 10.1186/s12915-022-01509-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 12/15/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case. RESULTS Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy's bone lesion and high mercury concentrations. CONCLUSIONS The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.
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Affiliation(s)
- Mohamed S Sarhan
- Eurac Research - Institute for Mummy Studies, 39100, Bolzano, Italy.
| | - Christina Wurst
- Eurac Research - Institute for Mummy Studies, 39100, Bolzano, Italy
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031, Basel, Switzerland
| | - Andreas J Bircher
- Department of Allergology, University Hospital Basel, 4031, Basel, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
| | - Holger Wittig
- Department of Biomedical Engineering, Institute of Forensic Medicine, University of Basel, 4056, Basel, Switzerland
| | - Thomas Briellmann
- Citizen Science Basel; formerly Institute of Forensic Medicine, Forensic Chemistry and Toxicology, University of Basel, 4056, Basel, Switzerland
| | - Marc Augsburger
- University Center of Legal Medicine, Lausanne, Geneva, Switzerland
| | - Gerhard Hotz
- Natural History Museum Basel, 4051, Basel, Switzerland
- Integrative Prehistory and Archaeological Science, University of Basel, 4056, Basel, Switzerland
| | - Albert Zink
- Eurac Research - Institute for Mummy Studies, 39100, Bolzano, Italy
| | - Frank Maixner
- Eurac Research - Institute for Mummy Studies, 39100, Bolzano, Italy.
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2
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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] [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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3
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Cheng Y, Lei W, Wang X, Tian Z, Liu H, Yang J, Lu S, Lai XH, Pu J, Huang Y, Zhang S, Yang C, Lian X, Bai Y, Wan K, Wang S, Xu J. Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov., two new rapidly growing mycobacterial species. Int J Syst Evol Microbiol 2021; 71. [PMID: 34878372 DOI: 10.1099/ijsem.0.005019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four bacterial strains (LJ126T/S18 and Z-34T/S20) recovered from faecal samples of Tibetan antelopes on the Qinghai-Tibet Plateau of China were analysed using a polyphasic approach. All four isolates were aerobic, short rod-shaped, non-motile, Gram-stain-positive, acid-fast and fast-growing. Phylogenetic analyses based upon 16S rRNA and whole-genome sequences showed that the two pair of strains formed two distinct branches within the evolutionary radiation of the genus Mycolicibacterium. Strains LJ126T/S18 and Z-34T/S20 were most closely related to Mycolicibacterium austroafricanum CCUG 37667T, Mycobacterium aurum NCTC 10437T, Mycobacterium pyrenivorans DSM 44605T, Mycobacterium monacense JCM 15658T, Mycolicibacterium sarraceniae JCM 30395T, Mycolicibacterium tokaiense JCM 6373T and Mycobacterium murale JCM 13392T, but readily distinguished from the known species by a combination of chemotaxonomic and phenotypic features and by low average nucleotide identity values (74.4-84.9 %). Consequently, the two strain pairs are considered to represent different novel species of Mycolicibacterium for which the names Mycolicibacterium baixiangningiae sp. nov. and Mycolicibacterium mengxianglii sp. nov. are proposed, with LJ126T (=CGMCC 1.1992T=KCTC 49535T) and Z-34T (=CGMCC 1.1993T=DSM 106172T) as the respective type strains.
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Affiliation(s)
- Yanpeng Cheng
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Wenjing Lei
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xiaoxia Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Zhi Tian
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Haican Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, Henan Province, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ying Huang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Sihui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, PR China
| | - Caixin Yang
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xingxing Lian
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yibo Bai
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Kanglin Wan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Suping Wang
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China
| | - Jianguo Xu
- Department of Epidemiology, Shanxi Medical University School of Public Health, Taiyuan, Shanxi 030001, PR China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.,Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Shanghai, 201508, PR China.,Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, PR China.,Department of Laboratorial Science and Technology & Vaccine Research Center, School of Public Health, Peking University, Beijing, 100191, PR China
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4
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Alarico S, Nunes-Costa D, Silva A, Costa M, Macedo-Ribeiro S, Empadinhas N. A genuine mycobacterial thermophile: Mycobacterium hassiacum growth, survival and GpgS stability at near-pasteurization temperatures. MICROBIOLOGY-SGM 2021; 166:474-483. [PMID: 32100712 DOI: 10.1099/mic.0.000898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Mycobacterium hassiacum is so far the most thermophilic among mycobacteria as it grows optimally at 50 °C and up to 65 °C in a glycerol-based medium, as verified in this study. Since this and other nontuberculous mycobacteria (NTM) thrive in diverse natural and artificial environments, from where they may access and infect humans, we deemed essential to probe M. hassiacum resistance to heat, a strategy routinely used to control microbial growth in water-supply systems, as well as in the food and drink industries. In addition to possibly being a threat in its own right in rare occasions, M. hassiacum is also a good surrogate for studying other NTM species more often associated with opportunistic infection, namely Mycobacterium avium and Mycobacterium abscessus as well as their strictly pathogenic counterparts Mycobacterium tuberculosis and Mycobacterium leprae. In this regard, this thermophilic species is likely to be useful as a source of stable proteins that may provide more detailed structures of potential drug targets. Here, we investigate M. hassiacum growth at near-pasteurization temperatures and at different pHs and also characterize its thermostable glucosyl-3-phosphoglycerate synthase (GpgS), an enzyme considered essential for M. tuberculosis growth and associated with both nitrogen starvation and thermal stress in different NTM species.
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Affiliation(s)
- Susana Alarico
- IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal.,CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Daniela Nunes-Costa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,PDBEB - PhD Programme in Biomedicine and Experimental Biology, Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Alexandra Silva
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Mafalda Costa
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Sandra Macedo-Ribeiro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Nuno Empadinhas
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
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5
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van der Loo C, Bartie C, Barnard TG, Potgieter N. Detection of Free-Living Amoebae and Their Intracellular Bacteria in Borehole Water before and after a Ceramic Pot Filter Point-of-Use Intervention in Rural Communities in South Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:3912. [PMID: 33917870 PMCID: PMC8068299 DOI: 10.3390/ijerph18083912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 11/21/2022]
Abstract
Free-living amoebae (FLA) are ubiquitous in nature, whereas amoeba-resistant bacteria (ARB) have evolved virulent mechanisms that allow them to resist FLA digestion mechanisms and survive inside the amoeba during hostile environmental conditions. This study assessed the prevalence of FLA and ARB species in borehole water before and after a ceramic point-of-use intervention in rural households. A total of 529 water samples were collected over a five-month period from 82 households. All water samples were subjected to amoebal enrichment, bacterial isolation on selective media, and molecular identification using 16S PCR/sequencing to determine ARB species and 18S rRNA PCR/sequencing to determine FLA species present in the water samples before and after the ceramic pot intervention. Several FLA species including Acanthamoeba spp. and Mycobacterium spp. were isolated. The ceramic pot filter removed many of these microorganisms from the borehole water. However, design flaws could have been responsible for some FLA and ARB detected in the filtered water. FLA and their associated ARB are ubiquitous in borehole water, and some of these species might be potentially harmful and a health risk to vulnerable individuals. There is a need to do more investigations into the health risk of these organisms after point-of-use treatment.
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Affiliation(s)
- Clarissa van der Loo
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2094, South Africa; (C.v.d.L.); (T.G.B.)
| | | | - Tobias George Barnard
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2094, South Africa; (C.v.d.L.); (T.G.B.)
| | - Natasha Potgieter
- Environmental Health, Domestic Hygiene and Microbial Pathogens Research Group, Department of Microbiology, University of Venda, Thohoyandou 1950, South Africa
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6
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Phenotypic and molecular characterisation of a novel species, Mycobacterium hubeiense sp., isolated from the sputum of a patient with secondary tuberculosis in Hubei of China. Epidemiol Infect 2020; 148:e49. [PMID: 32054545 PMCID: PMC7078510 DOI: 10.1017/s0950268820000436] [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] [Indexed: 11/29/2022] Open
Abstract
A new fast-growing mycobacterium, designated strain QGD101T, was isolated from the sputum of an 84-year-old man suspected of tuberculosis in Wuhan Medical Treatment Center, Hubei, China. This strain was a gram-staining-negative, aerobic, non-spore-forming and catalase-positive bacterium, which was further identified as the NTM by PNB and TCH tests. The moxifloxacin and levofloxacin exhibited strong suppressing function against QGD101T with MIC values of 0.06 and 0.125 µg/ml after drug susceptibility testing of six main antimicrobial agents on mycobacteria. Based on the sequence analysis of 16S rRNA, rpoB, hsp65 and 16S-23S rRNA internal transcribed spacer, the strain QGD101T could not be identified to a species level. Mycobacterium moriokaense ATCC43059T that shared the highest 16S rRNA gene sequence similarity (98%) with strain QGD101T was actually different in genomes average nucleotide identity (78.74%). In addition, the major cellular fatty acids of QGD101T were determined as C18:1ω9c, C16:0 and C18:2ω6c. The DNA G + C content was 64.9% measured by high performance liquid chromatography. Therefore, the phenotypic and genotypic characterisation of this strain led us to the conclusion that it represents a novel species of mycobacteria, for which the name Mycobacterium hubeiense sp. nov. (type strain QGD101T = CCTCCAA 2017003T = KCTC39927T) was proposed. Thus, the results of this study are very significant for the clinical diagnosis of tuberculosis and future personalised medicine.
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7
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Association of non-tuberculous mycobacteria with Mycobacterium leprae in environment of leprosy endemic regions in India. INFECTION GENETICS AND EVOLUTION 2019; 72:191-198. [DOI: 10.1016/j.meegid.2018.11.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/31/2018] [Accepted: 11/11/2018] [Indexed: 01/09/2023]
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8
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Pourahmad F, Adams A, Thompson KD, Richards RH. Identification of aquatic mycobacteria based on sequence analysis of the 16S–23S rRNA internal transcribed spacer region. J Med Microbiol 2019; 68:221-229. [DOI: 10.1099/jmm.0.000891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- F. Pourahmad
- 1School of Veterinary Sciences, Ilam University, PO Box 69315516, Ilam, Iran
| | - A. Adams
- 2Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
| | - K. D. Thompson
- 3Aquaculture Research Group, Moredun Research Institute, Pentlands Science Park Bush Loan, Penicuik, Midlothian, UK
| | - R. H. Richards
- 2Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
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9
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Description of a novel species of fast growing mycobacterium: Mycobacterium kyogaense sp. nov., a scotochromogenic strain received as Mycobacterium vaccae. Int J Syst Evol Microbiol 2018; 68:3726-3734. [DOI: 10.1099/ijsem.0.003039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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10
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Gupta RS, Lo B, Son J. Phylogenomics and Comparative Genomic Studies Robustly Support Division of the Genus Mycobacterium into an Emended Genus Mycobacterium and Four Novel Genera. Front Microbiol 2018; 9:67. [PMID: 29497402 PMCID: PMC5819568 DOI: 10.3389/fmicb.2018.00067] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023] Open
Abstract
The genus Mycobacterium contains 188 species including several major human pathogens as well as numerous other environmental species. We report here comprehensive phylogenomics and comparative genomic analyses on 150 genomes of Mycobacterium species to understand their interrelationships. Phylogenetic trees were constructed for the 150 species based on 1941 core proteins for the genus Mycobacterium, 136 core proteins for the phylum Actinobacteria and 8 other conserved proteins. Additionally, the overall genome similarity amongst the Mycobacterium species was determined based on average amino acid identity of the conserved protein families. The results from these analyses consistently support the existence of five distinct monophyletic groups within the genus Mycobacterium at the highest level, which are designated as the "Tuberculosis-Simiae," "Terrae," "Triviale," "Fortuitum-Vaccae," and "Abscessus-Chelonae" clades. Some of these clades have also been observed in earlier phylogenetic studies. Of these clades, the "Abscessus-Chelonae" clade forms the deepest branching lineage and does not form a monophyletic grouping with the "Fortuitum-Vaccae" clade of fast-growing species. In parallel, our comparative analyses of proteins from mycobacterial genomes have identified 172 molecular signatures in the form of conserved signature indels and conserved signature proteins, which are uniquely shared by either all Mycobacterium species or by members of the five identified clades. The identified molecular signatures (or synapomorphies) provide strong independent evidence for the monophyly of the genus Mycobacterium and the five described clades and they provide reliable means for the demarcation of these clades and for their diagnostics. Based on the results of our comprehensive phylogenomic analyses and numerous identified molecular signatures, which consistently and strongly support the division of known mycobacterial species into the five described clades, we propose here division of the genus Mycobacterium into an emended genus Mycobacterium encompassing the "Tuberculosis-Simiae" clade, which includes all of the major human pathogens, and four novel genera viz. Mycolicibacterium gen. nov., Mycolicibacter gen. nov., Mycolicibacillus gen. nov. and Mycobacteroides gen. nov. corresponding to the "Fortuitum-Vaccae," "Terrae," "Triviale," and "Abscessus-Chelonae" clades, respectively. With the division of mycobacterial species into these five distinct groups, attention can now be focused on unique genetic and molecular characteristics that differentiate members of these groups.
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Affiliation(s)
- Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, CA, Canada
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11
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Lee JC, Whang KS. Mycobacterium aquiterrae sp. nov., a rapidly growing bacterium isolated from groundwater. Int J Syst Evol Microbiol 2017; 67:4104-4110. [PMID: 28920836 DOI: 10.1099/ijsem.0.002261] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strain representing a rapidly growing, Gram-stain-positive, aerobic, rod-shaped, non-motile, non-sporulating and non-pigmented species of the genus Mycobacterium, designated strain S-I-6T, was isolated from groundwater at Daejeon in Korea. The strain grew at temperatures between 10 and 37 °C (optimal growth at 25 °C), between pH 4.0 and 9.0 (optimal growth at pH 7.0) and at salinities of 0-5 % (w/v) NaCl, growing optimally with 2 % (w/v) NaCl. Phylogenetic analyses based on multilocus sequence analysis of the 16S rRNAgene, hsp65, rpoB and the 16S-23S internal transcribed spacer indicated that strain S-I-6T belonged to the rapidly growing mycobacteria, being most closely related to Mycobacterium sphagni. On the basis of polyphasic taxonomic analysis, the bacterial strain was distinguished from its phylogenetic neighbours by chemotaxonomic properties and other biochemical characteristics. DNA-DNA relatedness among strain S-I-6T and the closest phylogenetic neighbour strongly support the proposal that this strain represents a novel species within the genus Mycobacterium, for which the name Mycobacterium aquiterrae sp. nov. is proposed. The type strain is S-I-6T (=KACC 17600T=NBRC 109805T=NCAIM B 02535T).
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Affiliation(s)
- Jae-Chan Lee
- Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea.,Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
| | - Kyung-Sook Whang
- Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea.,Institute of Microbial Ecology and Resources, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon 302-318, Republic of Korea
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12
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Sequence‐Based Identification and Characterization of Mycobacteria. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Comparison of culture methods for isolation of nontuberculous mycobacteria from surface waters. Appl Environ Microbiol 2010; 76:3514-20. [PMID: 20363776 DOI: 10.1128/aem.02659-09] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The environment is the likely source of most nontuberculous mycobacteria (NTM) involved in human infections, especially pulmonary, skin, and soft tissue infections. In order to measure the prevalence of NTM in different aquatic ecosystems, we tried to standardize the culture methods used for surface water testing since many procedures have been described previously. Cultivation of mycobacteria requires long-term incubation in rich media and inactivation of rapidly growing microorganisms whose growth impedes observation of mycobacterial colonies. Consequently, the two criteria used for evaluation of the methods examined were (i) the rate of inhibition of nontarget microorganisms and (ii) the efficiency of recovery of mycobacteria. We compared the competitive growth of Mycobacterium chelonae and M. avium with nontarget microorganisms on rich Middlebrook 7H11-mycobactin medium after treatment by several chemical decontamination methods that included acids, bases, detergent, or cetylpyridinium chloride (CPC) with and without an antibiotic cocktail, either PANTA (40 U/ml polymyxin, 4 microg/ml amphotericin B, 16 microg/ml nalidixic acid, 4 microg/ml trimethoprim, and 4 microg/ml azlocillin) or PANTAV (PANTA plus 10 microg/ml vancomycin). Our results showed that treatment for 30 min with CPC (final concentration, 0.05%) of water concentrated by centrifugation, followed by culture on a rich medium supplemented with PANTA, significantly decreased the growth of nontarget microorganisms (the concentrations were 6.2 +/- 0.4 log(10) CFU/liter on Middlebrook 7H11j medium and 4.2 +/- 0.2 log(10) CFU/liter on Middlebrook 7H11j medium containing PANTA [P < 0.001]), while the effect of this procedure on NTM was not as great (the concentrations of M. chelonae on the two media were 7.0 +/- 0.0 log(10) CFU/liter and 6.9 +/- 0.0 log(10) CFU/liter, respectively, and the concentrations of M. avium were 9.1 +/- 0.0 log(10) CFU/liter and 8.9 +/- 0.0 log(10) CFU/liter, respectively). We propose that this standardized culture procedure could be used for detection of NTM in aquatic samples.
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Abstract
The continuous evolution of mycobacterial taxonomy may represent a source of confusion for laboratories and clinicians. Apart from the obvious pathogenic strains of the Mycobacterium tuberculosis complex, Mycobacterium leprae and Mycobacterium ulcerans, the role of other mycobacteria may be associated with varying conditions ranging from contamination to specific disease processes. Of the more than 120 mycobacterial species recognized currently, very few have not been reported as pathogenic in humans or animals. Although the attempt to keep pace with the steadily increasing number of mycobacterial species seems hopeless, a careful review of the recent literature relevant to the newly described species may be advantageous. The aim of this present update is to provide epidemiological and clinical information along with major phenotypic and genotypic characteristics of the species described in the last 3 years.
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Affiliation(s)
- Enrico Tortoli
- Regional Reference Centre for Mycobacteria, Careggi Hospital, Florence, Italy.
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15
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Trujillo ME, Fernández-Molinero C, Velázquez E, Kroppenstedt RM, Schumann P, Mateos PF, Martínez-Molina E. Micromonospora mirobrigensis sp. nov. Int J Syst Evol Microbiol 2005; 55:877-880. [PMID: 15774678 DOI: 10.1099/ijs.0.63361-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An actinomycete strain was recovered from a pond where radon is known to be dissolved. A polyphasic study was undertaken to identify the new isolate. The 16S rRNA gene sequence of strain WA201T showed closest similarity to the type strains of Micromonospora carbonacea (98·5 %) and Micromonospora matsumotoense (98·1 %). The chemotaxonomic results confirmed the taxonomic position of the isolate in the genus Micromonospora. DNA–DNA relatedness values supported the classification of this isolate as a novel species. A number of physiological and biochemical tests were able to distinguish strain WA201T from its closest phylogenetic neighbours. Therefore, it is proposed that isolate WA201T (=DSM 44830T=LMG 22229T) be considered the type strain representing a novel species, Micromonospora mirobrigensis sp. nov.
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Affiliation(s)
- Martha E Trujillo
- Departamento de Microbiología y Genética, Edificio Departamental, Lab 209, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Carmen Fernández-Molinero
- Departamento de Microbiología y Genética, Edificio Departamental, Lab 209, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Edificio Departamental, Lab 209, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Reiner M Kroppenstedt
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Peter Schumann
- DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder Weg 1b, 38124 Braunschweig, Germany
| | - Pedro F Mateos
- Departamento de Microbiología y Genética, Edificio Departamental, Lab 209, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Eustoquio Martínez-Molina
- Departamento de Microbiología y Genética, Edificio Departamental, Lab 209, Campus Miguel de Unamuno, Universidad de Salamanca, 37007 Salamanca, Spain
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