1
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Kiepas AB, Hoskisson PA, Pritchard L. 16S rRNA phylogeny and clustering is not a reliable proxy for genome-based taxonomy in Streptomyces. Microb Genom 2024; 10. [PMID: 39254673 PMCID: PMC11385388 DOI: 10.1099/mgen.0.001287] [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] [Indexed: 09/11/2024] Open
Abstract
Streptomyces is among the most extensively studied genera of bacteria but its complex taxonomy remains contested and is suspected to contain significant species-level misclassification. Resolving the classification of Streptomyces would benefit many areas of applied microbiology that rely on an accurate ground truth for grouping of related organisms, including comparative genomics-based searches for novel antimicrobials. We survey taxonomic conflicts between 16S rRNA and whole genome-based Streptomyces classifications using 2276 publicly available Streptomyces genome assemblies and 48 981 publicly available full-length 16S rRNA Streptomyces sequences from silva, Greengenes, Ribosomal Database Project (RDP), and NCBI (National Centre for Biotechnology Information) databases. We construct a full-length 16S gene tree for 14 239 distinct Streptomyces sequences that resolves three major lineages of Streptomyces, but whose topology is not consistent with existing taxonomic assignments. We use these sequence data to delineate 16S and whole genome landscapes for Streptomyces, demonstrating that 16S and whole-genome classifications are frequently in disagreement, and that 16S zero-radius Operational Taxonomic Units (zOTUs) are often inconsistent with Average Nucleotide Identity (ANI)-based taxonomy. Our results strongly imply that 16S rRNA sequence data does not map to taxonomy sufficiently well to delineate Streptomyces species routinely. We propose that alternative marker sequences should be adopted by the community for classification and metabarcoding. Insofar as Streptomyces taxonomy has been determined or supported by 16S sequence data and may in parts be in error, we also propose that reclassification of the genus by alternative approaches may benefit the Streptomyces community.
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Affiliation(s)
- Angelika B Kiepas
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
| | - Leighton Pritchard
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow, G4 0RE, UK
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2
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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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3
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Jaiswal LK, Singh RK, Nayak T, Kakkar A, Kandwal G, Singh VS, Gupta A. A comparative analysis of mycobacterial ribonucleases: Towards a therapeutic novel drug target. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105645. [PMID: 39067582 DOI: 10.1016/j.meegid.2024.105645] [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: 03/22/2024] [Revised: 06/18/2024] [Accepted: 07/21/2024] [Indexed: 07/30/2024]
Abstract
Bacterial responses to continuously changing environments are addressed through modulation of gene expression at the level of transcription initiation, RNA processing and/or decay. Ribonucleases (RNases) are hydrolytic or phosphorolytic enzymes involved in a majority of RNA metabolism reactions. RNases play a crucial role in RNA degradation, either independently or in collaboration with various trans-acting regulatory factors. The genus Mycobacterium consists of five subgenera: Mycobacteroides, Mycolicibacterium, Mycobacterium, Mycolicibacter and Mycolicibacillus, which include 63 fully sequenced species (pathogenic/non-pathogenic) to date. These include 13 different RNases, among which 5 are exonucleases (RNase PH, PNPase, RNase D, nano-RNases and RNase AS) and 8 are endonucleases (RNase J, RNase H, RNase P, RNase III, RNase BN, RNase Z, RNase G and RNase E), although RNase J and RNase BN were later identified to have exoribonuclease functions also. Here, we provide a detailed comparative insight into the Escherichia coli and mycobacterial RNases with respect to their types, phylogeny, structure, function, regulation and mechanism of action, with the main emphasis on RNase E. Among these 13 different mycobacterial RNases, 10 are essential for cell survival and have diverse structures hence, they are promising drug targets. RNase E is also an essential endonuclease that is abundant in many bacteria, forms an RNA degradosome complex that controls central RNA processing/degradation and has a conserved 5' sensor domain/DNase-I like region in its RNase domain. The essential mycobacterial RNases especially RNase E provide a potential repertoire of drug targets that can be exploited for inhibitor/modulator screening against many deadly mycobacterial diseases.
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Affiliation(s)
- Lav Kumar Jaiswal
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi U.P.-221005, India
| | - Rakesh Kumar Singh
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi U.P.-221005, India
| | - Tanmayee Nayak
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi U.P.-221005, India
| | - Anuja Kakkar
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi U.P.-221005, India
| | - Garima Kandwal
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi U.P.-221005, India
| | - Vijay Shankar Singh
- Department of Microbiology, School of life Sciences, Sikkim University, Gangtok 737102, Sikkim, India
| | - Ankush Gupta
- Molecular Microbiology Laboratory, Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi U.P.-221005, India.
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4
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Bułacz H, Hołówka J, Wójcik W, Zakrzewska-Czerwińska J. MksB is a novel mycobacterial condensin that orchestrates spatiotemporal positioning of replication machinery. Sci Rep 2024; 14:19026. [PMID: 39152186 PMCID: PMC11329512 DOI: 10.1038/s41598-024-70054-w] [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: 05/07/2024] [Accepted: 08/12/2024] [Indexed: 08/19/2024] Open
Abstract
Condensins play important roles in maintaining bacterial chromatin integrity. In mycobacteria, three types of condensins have been characterized: a homolog of SMC and two MksB-like proteins, the recently identified MksB and EptC. Previous studies suggest that EptC contributes to defending against foreign DNA, while SMC and MksB may play roles in chromosome organization. Here, we report for the first time that the condensins, SMC and MksB, are involved in various DNA transactions during the cell cycle of Mycobacterium smegmatis (currently named Mycolicibacterium smegmatis). SMC appears to be required during the last steps of the cell cycle, where it contributes to sister chromosome separation. Intriguingly, in contrast to other bacteria, mycobacterial MksB follows replication forks during chromosome replication and hence may be involved in organizing newly replicated DNA.
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Affiliation(s)
- Hanna Bułacz
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
| | - Joanna Hołówka
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland.
| | - Wiktoria Wójcik
- Department of Molecular Microbiology, University of Wrocław, Wrocław, Poland
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5
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Parkkinen J, Bhowmik R, Tolvanen M, Carta F, Supuran CT, Parkkila S, Aspatwar A. Mycobacterial β-carbonic anhydrases: Molecular biology, role in the pathogenesis of tuberculosis and inhibition studies. Enzymes 2024; 55:343-381. [PMID: 39222997 DOI: 10.1016/bs.enz.2024.05.012] [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] [Indexed: 09/04/2024]
Abstract
Mycobacterium tuberculosis (Mtb), which causes tuberculosis (TB), is still a major global health problem. According to the World Health Organization (WHO), TB still causes more deaths worldwide than any other infectious agent. Drug-sensitive TB is treatable using first-line drugs; treatment of multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB requires second- and third-line drugs. However, due to the long duration of treatment, the noncompliance of patients with different levels of resistance of Mtb to these drugs has worsened the situation. Previously developed anti-TB drugs targeted the replication machinery, protein synthesis, and cell wall biosynthesis pathways of Mtb. Therefore, novel drugs targeting alternate pathways crucial for the survival and pathogenesis of Mtb in the human host are needed. The genome of Mtb encodes three β-carbonic anhydrases (CAs) that are fundamental for pH homeostasis, hypoxia, survival, and pathogenesis. Recently, several studies have shown that the β-CAs of Mtb could be inhibited both in vitro and in vivo using small chemical molecules, suggesting that these enzymes could be novel targets for developing anti-TB compounds that are devoid of resistance by Mtb. In addition, homologs of β-CAs are absent in humans; therefore, drugs developed to target these enzymes might have minimal off-target effects. In this work, we describe the roles of β-CAs in Mtb and discuss bioinformatics and cheminformatics tools used in development and discovery of novel inhibitors of these enzymes. In addition, we summarize the in vitro and in vivo studies demonstrating that the β-CAs of Mtb are indeed druggable targets.
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Affiliation(s)
- Jenny Parkkinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ratul Bhowmik
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | | | - Fabrizio Carta
- Neurofarba Department, Sezione di Chimica Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Firenze, Italy
| | - Claudiu T Supuran
- Neurofarba Department, Sezione di Chimica Farmaceutica e Nutraceutica, Università degli Studi di Firenze, Firenze, Italy
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Fimlab Ltd. and Tampere University Hospital, Tampere, Finland
| | - Ashok Aspatwar
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
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Maranha A, Alarico S, Nunes-Costa D, Melo-Marques I, Roxo I, Castanheira P, Caramelo O, Empadinhas N. Drinking Water Microbiota, Entero-Mammary Pathways, and Breast Cancer: Focus on Nontuberculous Mycobacteria. Microorganisms 2024; 12:1425. [PMID: 39065193 PMCID: PMC11279143 DOI: 10.3390/microorganisms12071425] [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: 05/29/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
The prospect of drinking water serving as a conduit for gut bacteria, artificially selected by disinfection strategies and a lack of monitoring at the point of use, is concerning. Certain opportunistic pathogens, notably some nontuberculous mycobacteria (NTM), often exceed coliform bacteria levels in drinking water, posing safety risks. NTM and other microbiota resist chlorination and thrive in plumbing systems. When inhaled, opportunistic NTM can infect the lungs of immunocompromised or chronically ill patients and the elderly, primarily postmenopausal women. When ingested with drinking water, NTM often survive stomach acidity, reach the intestines, and migrate to other organs using immune cells as vehicles, potentially colonizing tumor tissue, including in breast cancer. The link between the microbiome and cancer is not new, yet the recognition of intratumoral microbiomes is a recent development. Breast cancer risk rises with age, and NTM infections have emerged as a concern among breast cancer patients. In addition to studies hinting at a potential association between chronic NTM infections and lung cancer, NTM have also been detected in breast tumors at levels higher than normal adjacent tissue. Evaluating the risks of continued ingestion of contaminated drinking water is paramount, especially given the ability of various bacteria to migrate from the gut to breast tissue via entero-mammary pathways. This underscores a pressing need to revise water safety monitoring guidelines and delve into hormonal factors, including addressing the disproportionate impact of NTM infections and breast cancer on women and examining the potential health risks posed by the cryptic and unchecked microbiota from drinking water.
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Affiliation(s)
- Ana Maranha
- Center for Neuroscience and Cell Biology (CNC-UC), University of Coimbra, 3004-504 Coimbra, Portugal; (A.M.); (S.A.); (D.N.-C.); (I.M.-M.); (I.R.)
- Centre for Innovative Biomedicine & Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Susana Alarico
- Center for Neuroscience and Cell Biology (CNC-UC), University of Coimbra, 3004-504 Coimbra, Portugal; (A.M.); (S.A.); (D.N.-C.); (I.M.-M.); (I.R.)
- Centre for Innovative Biomedicine & Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Daniela Nunes-Costa
- Center for Neuroscience and Cell Biology (CNC-UC), University of Coimbra, 3004-504 Coimbra, Portugal; (A.M.); (S.A.); (D.N.-C.); (I.M.-M.); (I.R.)
- Centre for Innovative Biomedicine & Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Inês Melo-Marques
- Center for Neuroscience and Cell Biology (CNC-UC), University of Coimbra, 3004-504 Coimbra, Portugal; (A.M.); (S.A.); (D.N.-C.); (I.M.-M.); (I.R.)
- Centre for Innovative Biomedicine & Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Inês Roxo
- Center for Neuroscience and Cell Biology (CNC-UC), University of Coimbra, 3004-504 Coimbra, Portugal; (A.M.); (S.A.); (D.N.-C.); (I.M.-M.); (I.R.)
- Centre for Innovative Biomedicine & Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
- Ph.D. Programme in Biomedicine and Experimental Biology (PDBEB), Institute for Interdisciplinary Research, University of Coimbra, 3004-504 Coimbra, Portugal
| | | | - Olga Caramelo
- Gynecology Department, Coimbra Hospital and University Centre (CHUC), 3004-561 Coimbra, Portugal;
| | - Nuno Empadinhas
- Center for Neuroscience and Cell Biology (CNC-UC), University of Coimbra, 3004-504 Coimbra, Portugal; (A.M.); (S.A.); (D.N.-C.); (I.M.-M.); (I.R.)
- Centre for Innovative Biomedicine & Biotechnology (CIBB), University of Coimbra, 3004-504 Coimbra, Portugal
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7
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Vidyasagar, Patel RR, Singh SK, Dehari D, Nath G, Singh M. Facile green synthesis of silver nanoparticles derived from the medicinal plant Clerodendrum serratum and its biological activity against Mycobacterium species. Heliyon 2024; 10:e31116. [PMID: 38799742 PMCID: PMC11126841 DOI: 10.1016/j.heliyon.2024.e31116] [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: 09/10/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024] Open
Abstract
The emergence of multidrug-resistant mycobacterial strains is a significant crisis that has led to higher treatment failure rates and more toxic and expensive medications for tuberculosis (TB). The urgent need to develop novel therapeutics has galvanized research interest towards developing alternative antimicrobials such as silver nanoparticles (AgNPs). The current study focused on the anti-mycobacterial activity of green-synthesized AgNPs and its polyethylene glycol encapsulated derivative (PEG-AgNPs) with improved stability using the leaves extract of Clerodendrum serratum. Different characterization methods were used to analyze them. DLS analysis revealed a lower polydispersity index of PEG-AgNPs, suggesting a more uniform size distribution than that of AgNPs. The HR-TEM results revealed that the AgNPs and PEG-AgNPs have predominantly spherical shapes in the size range of 9-35 nm and 15-60 nm, respectively, while positive values of Zeta potential indicate their stability. FTIR-ATR analysis confirmed the presence of functional groups responsible for reducing and capping the bio-reduced AgNPs, whereas the XRD data established its crystalline nature. Impressively, the PEG-AgNPs exhibited maximum inhibitory activity against different Tubercular and Non-Tuberculous Mycobacterium species i.e., Mycobacterium smegmatis, Mycobacterium fortuitum and Mycobacterium marinum, relative to those of AgNPs and Linezolid. The flow cytometry assay showed that the anti-mycobacterial action was mediated by an increase in cell wall permeability. Notably, the results of AFM confirm their ability to inhibit mycobacterial biofilm significantly. We demonstrated the nontoxic nature of these AgNPs, explicated by the absence of hemolytic activity against human RBCs. Overall, the results suggest that PEG-AgNPs could offer a novel therapeutic approach with potential anti-mycobacterial activity and can overcome the limitations of existing TB therapies.
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Affiliation(s)
- Vidyasagar
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Ritu Raj Patel
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Sudhir Kumar Singh
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Deepa Dehari
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, Uttar Pradesh, 221005, India
| | - Gopal Nath
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
| | - Meenakshi Singh
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, 221005, India
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8
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Zhang L, Lin TY, Liu WT, Ling F. Toward Characterizing Environmental Sources of Non-tuberculous Mycobacteria (NTM) at the Species Level: A Tutorial Review of NTM Phylogeny and Phylogenetic Classification. ACS ENVIRONMENTAL AU 2024; 4:127-141. [PMID: 38765059 PMCID: PMC11100324 DOI: 10.1021/acsenvironau.3c00074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/27/2024] [Accepted: 01/29/2024] [Indexed: 05/21/2024]
Abstract
Nontuberculous mycobacteria (NTM) are any mycobacteria that do not cause tuberculosis or leprosy. While the majority of NTM are harmless and some of them are considered probiotic, a growing number of people are being diagnosed with NTM infections. Therefore, their detection in the environment is of interest to clinicians, environmental microbiologists, and water quality researchers alike. This review provides a tutorial on the foundational approaches for taxonomic classifications, with a focus on the phylogenetic relationships among NTM revealed by the 16S rRNA gene, rpoB gene, and hsp65 gene, and by genome-based approaches. Recent updates on the Mycobacterium genus taxonomy are also provided. A synthesis on the habitats of 189 mycobacterial species in a genome-based taxonomy framework was performed, with attention paid to environmental sources (e.g., drinking water, aquatic environments, and soil). The 16S rRNA gene-based classification accuracy for various regions was evaluated (V3, V3-V4, V3-V5, V4, V4-V5, and V1-V9), revealing overall excellent genus-level classification (up to 100% accuracy) yet only modest performance (up to 63.5% accuracy) at the species level. Future research quantifying NTM species in water systems, determining the effects of water treatment and plumbing conditions on their variations, developing high throughput species-level characterization tools for use in the environment, and incorporating the characterization of functions in a phylogenetic framework will likely fill critical knowledge gaps. We believe this tutorial will be useful for researchers new to the field of molecular or genome-based taxonomic profiling of environmental microbiomes. Experts may also find this review useful in terms of the selected key findings of the past 30 years, recent updates on phylogenomic analyses, as well as a synthesis of the ecology of NTM in a phylogenetic framework.
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Affiliation(s)
- Lin Zhang
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tzu-Yu Lin
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Wen-Tso Liu
- Department
of Civil and Environmental Engineering, University of Illinois, Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Fangqiong Ling
- Department
of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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9
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Wengenack NL, Brown-Elliott BA, Parrish NM, Salfinger M, Turenne CY, Wallace RJ, Zelazny AM. This is giving me a complex: a practical attempt to streamline nontuberculous mycobacteria nomenclature for clinical purposes. J Clin Microbiol 2024; 62:e0153123. [PMID: 38393324 PMCID: PMC10935656 DOI: 10.1128/jcm.01531-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024] Open
Affiliation(s)
- Nancy L. Wengenack
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Barbara A. Brown-Elliott
- Mycobacteria/Nocardia Research Laboratory, University of Texas at Tyler Health Science Center, School of Medicine Tyler, Tyler, Texas, USA
| | - Nicole M. Parrish
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Max Salfinger
- University of South Florida College of Public Health and Morsani College of Medicine, Tampa, Florida, USA
| | - Christine Y. Turenne
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Richard J. Wallace
- Mycobacteria/Nocardia Research Laboratory, University of Texas at Tyler Health Science Center, School of Medicine Tyler, Tyler, Texas, USA
| | - Adrian M. Zelazny
- Department of Laboratory Medicine, Microbiology Service, Clinical Center, NIH, Bethesda, Maryland, USA
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10
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Orgeur M, Sous C, Madacki J, Brosch R. Evolution and emergence of Mycobacterium tuberculosis. FEMS Microbiol Rev 2024; 48:fuae006. [PMID: 38365982 PMCID: PMC10906988 DOI: 10.1093/femsre/fuae006] [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: 11/09/2023] [Revised: 01/12/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases in human history, prevailing even in the 21st century. The causative agents of TB are represented by a group of closely related bacteria belonging to the Mycobacterium tuberculosis complex (MTBC), which can be subdivided into several lineages of human- and animal-adapted strains, thought to have shared a last common ancestor emerged by clonal expansion from a pool of recombinogenic Mycobacterium canettii-like tubercle bacilli. A better understanding of how MTBC populations evolved from less virulent mycobacteria may allow for discovering improved TB control strategies and future epidemiologic trends. In this review, we highlight new insights into the evolution of mycobacteria at the genus level, describing different milestones in the evolution of mycobacteria, with a focus on the genomic events that have likely enabled the emergence and the dominance of the MTBC. We also review the recent literature describing the various MTBC lineages and highlight their particularities and differences with a focus on host preferences and geographic distribution. Finally, we discuss on putative mechanisms driving the evolution of tubercle bacilli and mycobacteria in general, by taking the mycobacteria-specific distributive conjugal transfer as an example.
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Affiliation(s)
- Mickael Orgeur
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Camille Sous
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Jan Madacki
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Unit for Human Evolutionary Genetics, 75015 Paris, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
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11
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Romagnoli CL, Conceição EC, Machado E, Barreto LBPF, Sharma A, Silva NM, Marques LE, Juliano MA, da Silva Lourenço MC, Digiampietri LA, Suffys PN, Leão SC, Viana-Niero C. Description of new species of Mycobacterium terrae complex isolated from sewage at the São Paulo zoological park foundation in Brazil. Front Microbiol 2024; 15:1335985. [PMID: 38322314 PMCID: PMC10844392 DOI: 10.3389/fmicb.2024.1335985] [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: 11/09/2023] [Accepted: 01/02/2024] [Indexed: 02/08/2024] Open
Abstract
Five mycobacterial isolates from sewage were classified as members of the genus Mycobacterium but presented inconclusive species assignments. Thus, the isolates (MYC017, MYC098, MYC101, MYC123 and MYC340) were analyzed by phenotypical, biochemical, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and genomic features to clarify their taxonomic position. Phenotypic analysis and biochemical tests did not distinguish these isolates from other non-pigmented mycobacteria. In contrast, MALDI-TOF MS analysis showed that isolates were not related to any previously described Mycobacterium species. Comparative genomic analysis showed values of ANI and dDDH between 81.59-85.56% and 24.4-28.8%, respectively, when compared to the genomes of species of this genus. In addition, two (MYC101 and MYC123) presented indistinguishable protein spectra from each other and values of ANI = 98.57% and dDDH = 97.3%, therefore being considered as belonging to the same species. Phylogenetic analysis grouped the five isolates within the Mycobacterium terrae complex (MTC) but in a specific subclade and separated from the species already described and supported by 100% bootstrap value, confirming that they are part of this complex but different from earlier described species. According to these data, we propose the description of four new species belonging to the Mycobacterium genus: (i) Mycobacterium defluvii sp. nov. strain MYC017T (= ATCC TSD-296T = JCM 35364T), (ii) Mycobacterium crassicus sp. nov. strain MYC098T (= ATCC TSD-297T = JCM 35365T), (iii) Mycobacterium zoologicum sp. nov. strain MYC101T (= ATCC TSD-298T = JCM 35366T) and MYC123 (= ATCC BAA-3216 = JCM 35367); and (iv) Mycobacterium nativiensis sp. nov. strain MYC340T (= ATCC TSD-299T = JCM 35368T).
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Affiliation(s)
- Camila Lopes Romagnoli
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Emilyn Costa Conceição
- Laboratório de Bacteriologia e Bioensaios em Micobactérias, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Edson Machado
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Leonardo Bruno Paz Ferreira Barreto
- Laboratório de Bacteriologia e Bioensaios em Micobactérias, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Abhinav Sharma
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Natalia Maria Silva
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Lucas Evangelista Marques
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Maria Cristina da Silva Lourenço
- Laboratório de Bacteriologia e Bioensaios em Micobactérias, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Cristina Viana-Niero
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, São Paulo, Brazil
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12
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Hall MB, Coin LJM. Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data. Gigascience 2024; 13:giae010. [PMID: 38573185 PMCID: PMC10993716 DOI: 10.1093/gigascience/giae010] [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: 09/18/2023] [Revised: 01/10/2024] [Accepted: 02/27/2024] [Indexed: 04/05/2024] Open
Abstract
BACKGROUND Culture-free real-time sequencing of clinical metagenomic samples promises both rapid pathogen detection and antimicrobial resistance profiling. However, this approach introduces the risk of patient DNA leakage. To mitigate this risk, we need near-comprehensive removal of human DNA sequences at the point of sequencing, typically involving the use of resource-constrained devices. Existing benchmarks have largely focused on the use of standardized databases and largely ignored the computational requirements of depletion pipelines as well as the impact of human genome diversity. RESULTS We benchmarked host removal pipelines on simulated and artificial real Illumina and Nanopore metagenomic samples. We found that construction of a custom kraken database containing diverse human genomes results in the best balance of accuracy and computational resource usage. In addition, we benchmarked pipelines using kraken and minimap2 for taxonomic classification of Mycobacterium reads using standard and custom databases. With a database representative of the Mycobacterium genus, both tools obtained improved specificity and sensitivity, compared to the standard databases for classification of Mycobacterium tuberculosis. Computational efficiency of these custom databases was superior to most standard approaches, allowing them to be executed on a laptop device. CONCLUSIONS Customized pangenome databases provide the best balance of accuracy and computational efficiency when compared to standard databases for the task of human read removal and M. tuberculosis read classification from metagenomic samples. Such databases allow for execution on a laptop, without sacrificing accuracy, an especially important consideration in low-resource settings. We make all customized databases and pipelines freely available.
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Affiliation(s)
- Michael B Hall
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000 Victoria, Australia
| | - Lachlan J M Coin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000 Victoria, Australia
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13
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Špičić S, Duvnjak S, Papić B, Reil I, Zrnčić S, Mihaljević Ž, Naletilić Š, Zupičić IG, Kompes G, Habrun B, Mareković I, Zdelar-Tuk M. Description of Mycobacterium pinniadriaticum sp. nov., isolated from a noble pen shell ( Pinna nobilis) population in Croatia. Front Microbiol 2023; 14:1289182. [PMID: 38192290 PMCID: PMC10773828 DOI: 10.3389/fmicb.2023.1289182] [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: 09/05/2023] [Accepted: 11/17/2023] [Indexed: 01/10/2024] Open
Abstract
Introduction Shortly before the mass mortality event of the noble pen shell (Pinna nobilis) population in the south-eastern Adriatic coast, two rapidly growing Mycobacterium strains CVI_P3T (DSM 114013 T, ATCC TSD-295 T) and CVI_P4 were obtained from the organs of individual mollusks during the regular health status monitoring. Methods The strains were identified as members of the genus Mycobacterium using basic phenotypic characteristics, genus-specific PCR assays targeting the hsp65 and 16S rRNA genes and the commercial hybridization kit GenoType Mycobacterium CM (Hain Lifescience, Germany). MALDI-TOF mass spectrometry did not provide reliable identification using the Bruker Biotyper Database. Results and discussion Genome-wide phylogeny and average nucleotide identity (ANI) values confirmed that the studied strains are clearly differentiated from their closest phylogenetic relative Mycobacterium aromaticivorans and other validly published Mycobacterium species (ANI ≤ 85.0%). The type strain CVI_P3T was further characterized by a polyphasic approach using both phenotypic and genotypic methods. Based on the phenotypic, chemotaxonomic and phylogenetic results, we conclude that strains CVI_P3T and CVI_P4 represent a novel species, for which the name Mycobacterium pinniadriaticum sp. nov. is proposed.
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Affiliation(s)
- Silvio Špičić
- Laboratory for Bacterial Zoonosis and Molecular Diagnostics of Bacterial Diseases, Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Sanja Duvnjak
- Laboratory for Bacterial Zoonosis and Molecular Diagnostics of Bacterial Diseases, Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Bojan Papić
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Reil
- Laboratory for Bacterial Zoonosis and Molecular Diagnostics of Bacterial Diseases, Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Snježana Zrnčić
- Laboratory for Fish Pathology, Department for Pathological Morphology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Željko Mihaljević
- Laboratory for Pathology, Department for Pathological Morphology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Šimun Naletilić
- Laboratory for Pathology, Department for Pathological Morphology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Ivana Giovanna Zupičić
- Laboratory for Fish Pathology, Department for Pathological Morphology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Gordan Kompes
- Laboratory for General Bacteriology and Mycology, Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Boris Habrun
- Laboratory for General Bacteriology and Mycology, Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Ivana Mareković
- Department of Clinical and Molecular Microbiology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Maja Zdelar-Tuk
- Laboratory for Bacterial Zoonosis and Molecular Diagnostics of Bacterial Diseases, Department of Bacteriology and Parasitology, Croatian Veterinary Institute, Zagreb, Croatia
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Khare R, Brown-Elliott BA. Culture, Identification, and Antimicrobial Susceptibility Testing of Pulmonary Nontuberculous Mycobacteria. Clin Chest Med 2023; 44:743-755. [PMID: 37890913 DOI: 10.1016/j.ccm.2023.06.001] [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] [Indexed: 10/29/2023]
Abstract
Nontuberculous mycobacteria (NTM) typically cause opportunistic pulmonary infections and reliable laboratory results can assist with diagnosis of disease. Microscopy can detect acid-fast bacilli from specimens though it has poor sensitivity. Solid and liquid culture are used to grow NTM, which are identified by molecular or protein-based assays. Because culture has a long turnaround time, some assays are designed to identify NTM directly from sputum specimens. When indicated, phenotypic susceptibility testing should be performed by broth microdilution as per the guidelines from the Clinical Laboratory Standards Institute. Genotypic susceptibility methods may be used to decrease the turnaround time for some antimicrobials.
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Affiliation(s)
- Reeti Khare
- Mycobacteriology Laboratory, 1400 Jackson Street, National Jewish Health, Denver, CO 80238, USA.
| | - Barbara A Brown-Elliott
- The University of TX Health Science Center at Tyler, Mycobacteria/Nocardia Laboratory, 11937 US Highway 271, Tyler, TX 75708, USA
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15
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Kania K, Wόjcik K, Czekajewska J, Grzesiak M, Klesiewicz K. Molecular Identification of Strains within the Mycobacterium abscessus Complex and Determination of Resistance to Macrolides and Aminoglycosides. Pol J Microbiol 2023; 72:491-506. [PMID: 38103008 PMCID: PMC10725167 DOI: 10.33073/pjm-2023-048] [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: 09/15/2023] [Accepted: 11/11/2023] [Indexed: 12/17/2023] Open
Abstract
One of the most relevant and pathogenic groups among the rapidly growing mycobacteria (RGM) is Mycobacterium abscessus complex (MABC) that includes three subspecies: M. abscessus subsp. abscessus, M. abscessus subsp. bolletii, and M. abscessus subsp. massiliense. The aim of this study was the analysis of prevalence of MABC among other non-tuberculous mycobacteria isolated from patients in the Malopolska Region of Poland, between 2018 and 2021, as well as determination of their subspecies and molecular mechanisms of resistance to macrolides and aminoglycosides. The incidence of MABC was 5,4% (12/223). Eight strains were classified as M. abscessus subsp. abscessus, three as M. abscessus subsp. massiliense and one M. abscessus subsp. bolletii. Molecular analysis showed resistance to macrolides for eight strains of M. abscessus subsp. abscessus associated with erm(41)T28 gene mutations. One strain of M. abscessus subsp. abscessus showed resistance to macrolides (two mutations simultaneously: in erm(41)T28 and rrl genes) and aminoglycosides (point mutation in rrs gene). One strain of M. abscessus subs. bolletii was resistant to macrolides (erm(41)T28 mutation), whereas presented no mutations for aminoglycosides. M. abscessus subsp. massiliense reveal no mutations. High clarithromycin resistance of M. abscessus, determines the urgent need for susceptibility-based treatment. Molecular determination of resistance mechanisms to aminoglycosides and macrolides enables fast and accurate targeted treatment implementation.
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Affiliation(s)
- Katarzyna Kania
- Malopolska Central Laboratory of Tuberculosis Diagnostics, The St. John Paul II Specialist Hospital, Cracow, Poland
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Collegium Medicum, Cracow, Poland
| | - Katarzyna Wόjcik
- Malopolska Central Laboratory of Tuberculosis Diagnostics, The St. John Paul II Specialist Hospital, Cracow, Poland
| | - Joanna Czekajewska
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Collegium Medicum, Cracow, Poland
| | - Magdalena Grzesiak
- Laboratory of Microbiology, The St. John Paul II Specialist Hospital, Cracow, Poland
| | - Karolina Klesiewicz
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Jagiellonian University Collegium Medicum, Cracow, Poland
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16
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Val-Calvo J, Vázquez-Boland JA. Mycobacteriales taxonomy using network analysis-aided, context-uniform phylogenomic approach for non-subjective genus demarcation. mBio 2023; 14:e0220723. [PMID: 37796005 PMCID: PMC10653829 DOI: 10.1128/mbio.02207-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE A robust taxonomy is essential for the organized study of prokaryotes and the effective communication of microbial knowledge. The genus rank is the mainstay of biological classification as it brings together under a common name a group of closely related organisms sharing the same recent ancestry and similar characteristics. Despite the unprecedented resolution afforded by whole-genome sequencing in defining evolutionary relationships, a consensus approach for phylogenomics-based prokaryotic genus delineation remains elusive. Taxonomists use different demarcation criteria, sometimes leading to genus rank over-splitting and the creation of multiple new genera. This work reports a simple, reliable, and standardizable method that seeks to minimize subjectivity in genomics-based demarcation of prokaryotic genera, exemplified through application to the order Mycobacteriales. Formal descriptions of proposed taxonomic changes based on our study are included.
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Affiliation(s)
- Jorge Val-Calvo
- Microbial Pathogenesis Laboratory, Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - José A. Vázquez-Boland
- Microbial Pathogenesis Laboratory, Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, Scotland, United Kingdom
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17
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Abad L, Gauthier CH, Florian I, Jacobs-Sera D, Hatfull GF. The heterogenous and diverse population of prophages in Mycobacterium genomes. mSystems 2023; 8:e0044623. [PMID: 37791767 PMCID: PMC10654092 DOI: 10.1128/msystems.00446-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/18/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Mycobacterium species include several human pathogens and mycobacteriophages show potential for therapeutic use to control Mycobacterium infections. However, phage infection profiles vary greatly among Mycobacterium abscessus clinical isolates and phage therapies must be personalized for individual patients. Mycobacterium phage susceptibility is likely determined primarily by accessory parts of bacterial genomes, and we have identified the prophage and phage-related genomic regions across sequenced Mycobacterium strains. The prophages are numerous and diverse, especially in M. abscessus genomes, and provide a potentially rich reservoir of new viruses that can be propagated lytically and used to expand the repertoire of therapeutically useful phages.
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Affiliation(s)
- Lawrence Abad
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Christian H. Gauthier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Isabella Florian
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Deborah Jacobs-Sera
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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18
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Sharma A, Bansal S, Kumari N, Vashistt J, Shrivastava R. Comparative proteomic investigation unravels the pathobiology of Mycobacterium fortuitum biofilm. Appl Microbiol Biotechnol 2023; 107:6029-6046. [PMID: 37542577 DOI: 10.1007/s00253-023-12705-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/26/2023] [Accepted: 07/15/2023] [Indexed: 08/07/2023]
Abstract
Biofilm formation by Mycobacterium fortuitum causes serious threats to human health due to its increased contribution to nosocomial infections. In this study, the first comprehensive global proteome analysis of M. fortuitum was reported under planktonic and biofilm growth states. A label-free Q Exactive Quadrupole-Orbitrap tandem mass spectrometry analysis was performed on the protein lysates. The differentially abundant proteins were functionally characterized and re-annotated using Blast2GO and CELLO2GO. Comparative analysis of the proteins among two growth states provided insights into the phenotypic switch, and fundamental pathways associated with pathobiology of M. fortuitum biofilm, such as lipid biosynthesis and quorum-sensing. Interaction network generated by the STRING database revealed associations between proteins that endure M. fortuitum during biofilm growth state. Hypothetical proteins were also studied to determine their functional alliance with the biofilm phenotype. CARD, VFDB, and PATRIC analysis further showed that the proteins upregulated in M. fortuitum biofilm exhibited antibiotic resistance, pathogenesis, and virulence. Heatmap and correlation analysis provided the biomarkers associated with the planktonic and biofilm growth of M. fortuitum. Proteome data was validated by qPCR analysis. Overall, the study provides insights into previously unexplored biochemical pathways that can be targeted by novel inhibitors, either for shortened treatment duration or for eliminating biofilm of M. fortuitum and related nontuberculous mycobacterial pathogens. KEY POINTS: • Proteomic analyses of M. fortuitum reveals novel biofilm markers. • Acetyl-CoA acetyltransferase acts as the phenotype transition switch. • The study offers drug targets to combat M. fortuitum biofilm infections.
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Affiliation(s)
- Ayushi Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, H.P, India
| | - Saurabh Bansal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, H.P, India
| | - Neha Kumari
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, H.P, India
| | - Jitendraa Vashistt
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, H.P, India
| | - Rahul Shrivastava
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173234, H.P, India.
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19
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Ruedas-López A, Tato M, Broncano-Lavado A, Esteban J, Ruiz-Serrano MJ, Sánchez-Cueto M, Toro C, Domingo D, Cacho J, Barrado L, López-Roa P. Subspecies Distribution and Antimicrobial Susceptibility Testing of Mycobacterium abscessus Clinical Isolates in Madrid, Spain: a Retrospective Multicenter Study. Microbiol Spectr 2023; 11:e0504122. [PMID: 37212700 PMCID: PMC10269645 DOI: 10.1128/spectrum.05041-22] [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: 12/07/2022] [Accepted: 04/12/2023] [Indexed: 05/23/2023] Open
Abstract
Mycobacterium abscessus (MABS) is the most pathogenic and drug-resistant rapidly growing mycobacteria. However, studies on MABS epidemiology, especially those focusing on subspecies level, are scarce. We aimed to determine MABS subspecies distribution and its correlation with phenotypic and genotypic antibiotic profiles. A retrospective multicenter study of 96 clinical MABS isolates in Madrid between 2016 to 2021 was conducted. Identification at the subspecies level and resistance to macrolides and aminoglycosides were performed by the GenoType NTM-DR assay. The MICs of 11 antimicrobials tested against MABS isolates were determined using the broth microdilution method (RAPMYCOI Sensititer titration plates). Clinical isolates included 50 (52.1%) MABS subsp. abscessus; 33 (34.4%) MABS subsp. massiliense; and 13 (13.5%) MABS subsp. bolletii. The lowest resistance rates corresponded to amikacin (2.1%), linezolid (6.3%), cefoxitin (7.3%), and imipenem (14.6%), and the highest to doxycycline (100.0%), ciprofloxacin (89.6%), moxifloxacin (82.3%), cotrimoxazole (82.3%), tobramycin (81.3%), and clarithromycin (50.0% at day 14 of incubation). Regarding tigecycline, although there are no susceptibility breakpoints, all strains but one showed MICs ≤ 1 μg/mL. Four isolates harbored mutations at positions 2058/9 of the rrl gene, one strain harbored a mutation at position 1408 of the rrl gene, and 18/50 harbored the T28C substitution at erm(41) gene. Agreement of the GenoType results with clarithromycin and amikacin susceptibility testing was 99.0% (95/96). The rate of MABS isolates showed an upward trend during the study period, being M. abscessus subsp. abscessus the most frequently isolated subspecies. Amikacin, cefoxitin, linezolid, and imipenem showed great in vitro activity. The GenoType NTM-DR assay provides a reliable and complementary tool to broth microdilution for drug resistance detection. IMPORTANCE Infections caused by Mycobacterium abscessus (MABS) are increasingly being reported worldwide. Identifying MABS subspecies and assessing their phenotypic resistance profiles are crucial for optimal management and better patient outcomes. M. abscessus subspecies differ in erm(41) gene functionality, which is a critical determinant of macrolide resistance. Additionally, resistance profiles of MABS and the subspecies distribution can vary geographically, highlighting the importance of understanding local epidemiology and resistance patterns. This study provides valuable insights into the epidemiology and resistance patterns of MABS and its subspecies in Madrid. Elevated resistance rates were observed for several recommended antimicrobials, emphasizing the need for cautious drug use. Furthermore, we assessed the GenoType NTM-DR assay, which examines principal mutations in macrolides and aminoglycosides resistance-related genes. We observed a high level of agreement between the GenoType NTM-DR assay and the microdilution method, indicating its usefulness as an initial tool for early initiation of appropriate therapy.
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Affiliation(s)
- Alba Ruedas-López
- Clinical Microbiology and Parasitology Department, Instituto de Investigación, Hospital Universitario, Madrid, Spain.
| | - Marta Tato
- Clinical Microbiology and Parasitology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Antonio Broncano-Lavado
- Clinical Microbiology and Parasitology Department, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Jaime Esteban
- Clinical Microbiology and Parasitology Department, Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades infecciosas CIBERINFEC, Spain
| | - María Jesús Ruiz-Serrano
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
- Clinical Microbiology and Infectious Diseases, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM) Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias- CIBERES (CB06/06/0058), Madrid, Spain
| | - María Sánchez-Cueto
- Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
- Clinical Microbiology and Infectious Diseases, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM) Madrid, Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Respiratorias- CIBERES (CB06/06/0058), Madrid, Spain
| | - Carlos Toro
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz, Madrid, Spain
| | - Diego Domingo
- Clinical Microbiology and Parasitology Department, Hospital Universitario de La Princesa, Madrid, Spain
| | - Juana Cacho
- Clinical Microbiology and Parasitology Department, Hospital Universitario de Getafe, Madrid, Spain
| | - Laura Barrado
- Clinical Microbiology and Parasitology Department, Hospital Universitario de Móstoles, Madrid, Spain
| | - Paula López-Roa
- Clinical Microbiology and Parasitology Department, Instituto de Investigación, Hospital Universitario, Madrid, Spain.
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20
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Mu Y, Qi W, Zhang T, Zhang J, Mao S. Coordinated response of milk bacterial and metabolic profiles to subacute ruminal acidosis in lactating dairy cows. J Anim Sci Biotechnol 2023; 14:60. [PMID: 37138330 PMCID: PMC10158360 DOI: 10.1186/s40104-023-00859-8] [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: 10/19/2022] [Accepted: 03/01/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Bovine milk is an important source of nutrition for human consumption, and its quality is closely associated with the microbiota and metabolites in it. But there is limited knowledge about the milk microbiome and metabolome in cows with subacute ruminal acidosis. METHODS Eight ruminally cannulated Holstein cows in mid lactation were selected for a 3-week experiment. The cows were randomly allocated into 2 groups, fed either a conventional diet (CON; 40% concentrate; dry matter basis) or a high-concentrate diet (HC; 60% concentrate; dry matter basis). RESULTS The results showed that there was a decreased milk fat percentage in the HC group compared to the CON group. The amplicon sequencing results indicated that the alpha diversity indices were not affected by the HC feeding. At the phylum level, the milk bacteria were dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes both in the CON and HC groups. At the genus level, the HC cows displayed an improved proportion of Labrys (P = 0.015) compared with the CON cows. Results of both the principal components analysis and partial least squares of discriminant analysis of milk metabolome revealed that samples of the CON and HC groups clustered separately. A total of 31 differential metabolites were identified between the two groups. Of these, the levels of 11 metabolites decreased (α-linolenic acid, prostaglandin E2, L-lactic acid, L-malic acid, 3-hydroxysebacic acid, succinyladenosine, guanosine, pyridoxal, L-glutamic acid, hippuric acid, and trigonelline), whereas the levels of the other 20 metabolites increased in the HC group with respect to the CON group (P < 0.05). CONCLUSION These results suggested that subacute ruminal acidosis less impacted the diversity and composition of milk microbiota, but altered the milk metabolic profiles, which led to the decline of the milk quality.
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Affiliation(s)
- Yingyu Mu
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wangpan Qi
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tao Zhang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiyou Zhang
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shengyong Mao
- Ruminant Nutrition and Feed Engineering Technology Research Center, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
- Laboratory of Gastrointestinal Microbiology, Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, National Center for International Research on Animal Gut Nutrition, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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21
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Draft Genome Sequence of a Mycobacterium chelonae subsp. bovis Strain Isolated from a Baikal Seal (Pusa sibirica) in Captivity. Microbiol Resour Announc 2023; 12:e0113522. [PMID: 36840582 PMCID: PMC10019254 DOI: 10.1128/mra.01135-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Mycobacterium chelonae is a nontuberculous mycobacterium that causes infections in various animals, including humans. In this study, we report the draft genome sequence of M. chelonae subsp. bovis strain NJB1701, which was isolated from a Baikal seal (Pusa sibirica) in captivity in Japan.
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22
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Hunkins JJ, de-Moura VCN, Eddy JJ, Daley CL, Khare R. In vitro susceptibility patterns for rapidly growing nontuberculous mycobacteria in the United States. Diagn Microbiol Infect Dis 2023; 105:115882. [PMID: 36610383 DOI: 10.1016/j.diagmicrobio.2022.115882] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/01/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Antimicrobial susceptibility testing for rapidly growing mycobacteria (RGM) is uncommon or only performed in large reference laboratories. Here we developed a cumulative antibiogram for 14 RGM using the largest sample size to date (N = 3860). All RGM showed 82% to 100% susceptibility to amikacin. Mycobacterium abscessus showed low percentages of susceptibility to most antimicrobials; of antimicrobials without interpretations, the minimum inhibitory concentration-90 for clofazimine was low (≤0.5mg/L). All three subspecies had ≤2.6% rrl resistance mutations, however intact erm(41) was detected in 70% to100% of M. abscessus abscessus and bolletii. Mycobacterium chelonae had a similar susceptibility pattern to M. abscessus subsp. massiliense and Mycobacterium immunogenum except that it was susceptible to tobramycin (87%). Mycobacterium fortuitum complex and similar organisms showed higher frequency of susceptibility to fluoroquinolones, beta-lactams, linezolid, and trimethoprim/sulfamethoxazole. Although relatively small published RGM antibiograms showed substantial variance, a comprehensive antibiogram can help influence treatment and monitoring patterns of resistance.
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Affiliation(s)
- Joshua-J Hunkins
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO, USA
| | | | - Jared-J Eddy
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Charles-L Daley
- Department of Medicine, National Jewish Health, Denver, CO, USA; Department of Medicine, University of Colorado, Aurora, CO, USA
| | - Reeti Khare
- Advanced Diagnostics Laboratories, National Jewish Health, Denver, CO, USA; Department of Medicine, National Jewish Health, Denver, CO, USA.
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23
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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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24
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Renau-Mínguez C, Herrero-Abadía P, Ruiz-Rodriguez P, Sentandreu V, Torrents E, Chiner-Oms Á, Torres-Puente M, Comas I, Julián E, Coscolla M. Genomic analysis of Mycobacterium brumae sustains its nonpathogenic and immunogenic phenotype. Front Microbiol 2023; 13:982679. [PMID: 36687580 PMCID: PMC9850167 DOI: 10.3389/fmicb.2022.982679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/06/2022] [Indexed: 01/07/2023] Open
Abstract
Mycobacterium brumae is a rapid-growing, non-pathogenic Mycobacterium species, originally isolated from environmental and human samples in Barcelona, Spain. Mycobacterium brumae is not pathogenic and it's in vitro phenotype and immunogenic properties have been well characterized. However, the knowledge of its underlying genetic composition is still incomplete. In this study, we first describe the 4 Mb genome of the M. brumae type strain ATCC 51384T assembling PacBio reads, and second, we assess the low intraspecies variability by comparing the type strain with Illumina reads from three additional strains. Mycobacterium brumae genome is composed of a circular chromosome with a high GC content of 69.2% and containing 3,791 CDSs, 97 pseudogenes, one prophage and no CRISPR loci. Mycobacterium brumae has shown no pathogenic potential in in vivo experiments, and our genomic analysis confirms its phylogenetic position with other non-pathogenic and rapid growing mycobacteria. Accordingly, we determined the absence of virulence-related genes, such as ESX-1 locus and most PE/PPE genes, among others. Although the immunogenic potential of M. brumae was proved to be as high as Mycobacterium bovis BCG, the only mycobacteria licensed to treat cancer, the genomic content of M. tuberculosis T cell and B cell antigens in M. brumae genome is considerably lower than those antigens present in M. bovis BCG genome. Overall, this work provides relevant genomic data on one of the species of the mycobacterial genus with high therapeutic potential.
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Affiliation(s)
| | - Paula Herrero-Abadía
- Genetics and Microbiology Department, Faculty of Biosciences, Autonomous University of Barcelona, Barcelona, Spain
| | | | - Vicente Sentandreu
- Genomics Unit, Central Service for Experimental Research (SCSIE), University of Valencia, Burjassot, Spain
| | - Eduard Torrents
- Bacterial Infections and Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
- Microbiology Section, Department of Genetics, Microbiology, and Statistics, Biology Faculty, Universitat de Barcelona, Barcelona, Spain
| | | | | | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Esther Julián
- Genetics and Microbiology Department, Faculty of Biosciences, Autonomous University of Barcelona, Barcelona, Spain
| | - Mireia Coscolla
- I2SysBio, University of Valencia-FISABIO Joint Unit, Paterna, Spain
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25
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Updated Review on the Mechanisms of Pathogenicity in Mycobacterium abscessus, a Rapidly Growing Emerging Pathogen. Microorganisms 2022; 11:microorganisms11010090. [PMID: 36677382 PMCID: PMC9866562 DOI: 10.3390/microorganisms11010090] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023] Open
Abstract
In recent years, Mycobacterium abscessus has appeared as an emerging pathogen, with an increasing number of disease cases reported worldwide that mainly occur among patients with chronic lung diseases or impaired immune systems. The treatment of this pathogen represents a challenge due to the multi-drug-resistant nature of this species and its ability to evade most therapeutic approaches. However, although predisposing host factors for disease are well known, intrinsic pathogenicity mechanisms of this mycobacterium are still not elucidated. Like other mycobacteria, intracellular invasiveness and survival inside different cell lines are pathogenic factors related to the ability of M. abscessus to establish infection. Some of the molecular factors involved in this process are well-known and are present in the mycobacterial cell wall, such as trehalose-dimycolate and glycopeptidolipids. The ability to form biofilms is another pathogenic factor that is essential for the development of chronic disease and for promoting mycobacterial survival against the host immune system or different antibacterial treatments. This capability also seems to be related to glycopeptidolipids and other lipid molecules, and some studies have shown an intrinsic relationship between both pathogenic mechanisms. Antimicrobial resistance is also considered a mechanism of pathogenicity because it allows the mycobacterium to resist antimicrobial therapies and represents an advantage in polymicrobial biofilms. The recent description of hyperpathogenic strains with the potential interhuman transmission makes it necessary to increase our knowledge of pathogenic mechanisms of this species to design better therapeutic approaches to the management of these infections.
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26
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Survey of mycobacterial fluoroquinolone resistance protein conservon (mfp conservon) in Mycobacteriaceae and identification of its promoter activity. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Musser E, Smith C, Halse TA, Kohlerschmidt D, Rourke A, Fiero A, Musser KA, Escuyer V, Lapierre P. Characterization of Mycobacterium salfingeri sp. nov.: A novel nontuberculous mycobacteria isolated from a human wound infection. Front Microbiol 2022; 13:992610. [PMID: 36299734 PMCID: PMC9589434 DOI: 10.3389/fmicb.2022.992610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are environmental bacteria commonly found in soil and water in almost every part of the world. While usually non-pathogenic, they can cause acute respiratory and cutaneous infections under certain circumstances or in patients with underlying medical conditions. Contrary to members of the Mycobacterium tuberculosis complex, documented human-to-human transmissions of NTM have been rarely reported and most cases result from direct environmental exposure. Here we describe the identification of a new NTM species isolated from a hand laceration of a New York State patient after a fall. This new NTM forms rough, orange pigmented colonies and is naturally resistant to doxycycline and tobramycin. Whole genome analysis reveal no close relatives present in public databases, and our findings are in accordance with the recognition of a new taxonomic species of NTM. We propose the name Mycobacterium salfingeri sp. nov. for this new NTM representative. The type strain is 20-157661T (DSM = 113368T, BCCM = ITM 501207T).
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28
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He Y, Li J, Yu W, Zheng Y, Yang D, Xu Y, Zhao L, Ma X, Gong P, Gao Z. Characteristics of lower respiratory tract microbiota in the patients with post-hematopoietic stem cell transplantation pneumonia. Front Cell Infect Microbiol 2022; 12:943317. [PMID: 36176576 PMCID: PMC9513191 DOI: 10.3389/fcimb.2022.943317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/23/2022] [Indexed: 11/25/2022] Open
Abstract
Background Pneumonia is a leading cause of non-relapse mortality after hematopoietic stem cell transplantation (HSCT), and the lower respiratory tract (LRT) microbiome has been proven to be associated with various respiratory diseases. However, little is known about the characteristics of the LRT microbiome in patients with post-HSCT compared to healthy controls (HC) and community-acquired pneumonia (CAP). Methods Bronchoalveolar lavage samples from 55 patients with post-HSCT pneumonia, 44 patients with CAP, and 30 healthy volunteers were used to detect microbiota using 16S rRNA gene sequencing. Results The diversity of the LRT microbiome significantly decreased in patients with post-HSCT pneumonia, and the overall community was different from the CAP and HC groups. At the phylum level, post-HSCT pneumonia samples had a high abundance of Actinobacteria and a relatively low abundance of Bacteroidetes. The same is true for non-survivors compared with survivors in patients with post-HSCT pneumonia. At the genus level, the abundances of Pseudomonas, Acinetobacter, Burkholderia, and Mycobacterium were prominent in the pneumonia group after HSCT. On the other hand, gut-associated bacteria, Enterococcus were more abundant in the non-survivors. Some pathways concerning amino acid and lipid metabolism were predicted to be altered in patients with post-HSCT pneumonia. Conclusions Our results reveal that the LRT microbiome in patients with post-HSCT pneumonia differs from CAP patients and healthy controls, which could be associated with the outcome. The LRT microbiota could be a target for intervention during post-HSCT pneumonia.
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Affiliation(s)
- Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Jia Li
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yali Zheng
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
- Department of Respiratory, Critical Care, and Sleep Medicine, Xiang'an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Donghong Yang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yu Xu
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Lili Zhao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Xinqian Ma
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Pihua Gong
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
- *Correspondence: Pihua Gong, ; Zhancheng Gao,
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
- *Correspondence: Pihua Gong, ; Zhancheng Gao,
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29
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Kumar S, Sethi SK. Genome-based reclassification of Streptococcus ursoris as a later heterotypic synonym of Streptococcus ratti. Arch Microbiol 2022; 204:405. [PMID: 35723755 DOI: 10.1007/s00203-022-03012-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
Among the species of genus Streptococcus two members namely Streptococcus ratti and Streptococcus ursoris were isolated from oral cavity of rat and bear, respectively. Type strain of these members shows a 16S rRNA gene sequence similarity of 98.9%. Based on systematic phylo-taxonogenomics investigations, we could deduce the taxonomic assignment of the members of these species. Genome similarity assessment among the type strain of these members using average nucleotide identity (orthoANI and fastANI), digital DNA-DNA hybridization and average amino acid identity (AAI) were 98.5, 98.3, 88, and 98.3% respectively. All these values exceed the species delineation cutoffs suggesting a unified species. Phylogenetic tree obtained using 16S rRNA gene sequence also indicates the monophyletic nature of the member strains. Such monophyletic taxonomic positioning of the strains was further complemented with the whole genome-based phylogenomic tree. Based on these evidences, we propose S. ursoris should be reclassified as a later heterotypic synonym of S. ratti.
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Affiliation(s)
- Sanjeet Kumar
- School of Biotechnology, Gangadhar Meher University, Sambalpur, Odisha, 768004, India
| | - Santosh K Sethi
- School of Biotechnology, Gangadhar Meher University, Sambalpur, Odisha, 768004, India.
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30
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Sur S, Patra T, Karmakar M, Banerjee A. Mycobacterium abscessus: insights from a bioinformatic perspective. Crit Rev Microbiol 2022:1-16. [PMID: 35696783 DOI: 10.1080/1040841x.2022.2082268] [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: 11/03/2022]
Abstract
Mycobacterium abscessus is a nontuberculous mycobacterium, associated with broncho-pulmonary infections in individuals suffering from cystic fibrosis, bronchiectasis, and pulmonary diseases. The risk factors for transmission include biofilms, contaminated water resources, fomites, and infected individuals. M. abscessus is extensively resistant to antibiotics. To date, there is no vaccine and combination antibiotic therapy is followed. However, drug toxicities, low cure rates, and high cost of treatment make it imperfect. Over the last 20 years, bioinformatic studies on M. abscessus have advanced our understanding of the pathogen. This review integrates knowledge from the analysis of genomes, microbiomes, genomic variations, phylogeny, proteome, transcriptome, secretome, antibiotic resistance, and vaccine design to further our understanding. The utility of genome-based studies in comprehending disease progression, surveillance, tracing transmission routes, and epidemiological outbreaks on a global scale has been highlighted. Furthermore, this review underlined the importance of using computational methodologies for pinpointing factors responsible for pathogen survival and resistance. We reiterate the significance of interdisciplinary research to fight M. abscessus. In a nutshell, the outcome of computational studies can go a long way in creating novel therapeutic avenues to control M. abscessus mediated pulmonary infections.
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Affiliation(s)
- Saubashya Sur
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
| | - Tanushree Patra
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
| | - Mistu Karmakar
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
| | - Anindita Banerjee
- Postgraduate Department of Botany, Ramananda College, Bishnupur, India
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Mycolicibacter acidiphilus sp. nov., an extremely acid-tolerant member of the genus Mycolicibacter. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005419] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A nonmotile, facultatively anaerobic and rod-shaped bacterial strain, designated M1T was isolated from a bioreactor being operated at pH ~2 at Brisbane, Australia. Colonies appeared to be convex and white. Phylogenetic analysis of its genome revealed an affiliation with the genus
Mycolicibacter
and its closest species based on 16S rRNA gene analysis were
Mycolicibacter algericus
DSM 45454T (98.8 % similarity) and
Mycolicibacter terrae
CIP 104321T (98.8 %) with which strain M1T shared average nucleotide identity of 81.2 % and digital DNA–DNA hybridization similarity of 23.8 %. Strain M1T grew optimally at 0 % NaCl, at pH 6 and at between 30–33 °C. The polar lipid profile of strain M1T consisted of diphosphatidylglycerol, aminophosphoglycolipid, phosphatidylcholine, phospholipid, aminolipid, phosphoglyolipid, phosphatidylglycerol, two unidentified glycolipids and four unidentified lipids. The dominant cellular fatty acids (>10 %) were C16 : 0 and C18 : 1
ω9c and summed feature 7 (C19 : 1
ω7c and/or C19 : 1
ω6c). The DNA G+C content of strain M1T was 69.1 mol%. Based on in silico phylogenomic analysis coupled with physiological and chemotaxonomic characterizations, we classify strain M1T as representing a novel species within the genus
Mycolicibacter
, for which the name Mycolicibacter acidiphilus nov. is proposed. The type strain is M1T (=MCCC 1H00416T=KCTC 49392T).
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To Be or Not to Be Mesophilic, That Is the Question for Aeromonas salmonicida. Microorganisms 2022; 10:microorganisms10020240. [PMID: 35208695 PMCID: PMC8879556 DOI: 10.3390/microorganisms10020240] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 02/05/2023] Open
Abstract
The bacterium Aeromonas salmonicida has long been known to be one of the most feared pathogens in fish farming. However, the more we discover about this bacterial species, the more we question whether it is really exclusively an aquatic pathogen. In recent years, it has become obvious that this bacterial species includes a myriad of strains with various lifestyle and ecological niches, including the well-known strict psychrophiles, the first bacteria known of the species, and the newly described mesophilic strains. The mesophiles are able to grow at low temperatures, but even better at temperatures of approximately 37 °C, which strict psychrophiles cannot do. In this perspective article, we address some aspects surrounding this dual lifestyle in A. salmonicida, including the impact of mobile genetic elements, and how future research around this bacterial species may focus on the psychrophilic/mesophilic dichotomy, which makes A. salmonicida an increasingly interesting and relevant model for the study of speciation.
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