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Mon ML, Romano N, Farace PD, Tortone CA, Oriani DS, Picariello G, Zumárraga MJ, Gioffré AK, Talia PM. Exploring the cellulolytic activity of environmental mycobacteria. Tuberculosis (Edinb) 2024; 147:102516. [PMID: 38735123 DOI: 10.1016/j.tube.2024.102516] [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: 01/05/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Although studies on non-tuberculous mycobacteria have increased in recent years because they cause a considerable proportion of infections, their cellulolytic system is still poorly studied. This study presents a characterization of the cellulolytic activities of environmental mycobacterial isolates derived from soil and water samples from the central region of Argentina, aimed to evaluate the conservation of the mechanism for the degradation of cellulose in this group of bacteria. The molecular and genomic identification revealed identity with Mycolicibacterium septicum. The endoglucanase and total cellulase activities were assessed both qualitatively and quantitatively and the optimal enzymatic conditions were characterized. A specific protein of around 56 kDa with cellulolytic activity was detected in a zymogram. Protein sequences possibly arising from a cellulase were identified by mass spectrometry-based shotgun proteomics. Results showed that M. septicum encodes for cellulose- and hemicellulose-related degrading enzymes, including at least an active β-1,4 endoglucanase enzyme that could be useful to improve its survival in the environment. Given the important health issues related to mycobacteria, the results of the present study may contribute to the knowledge of their cellulolytic system, which could be important for their ability to survive in many different types of environments.
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Affiliation(s)
- María Laura Mon
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Nelson Romano
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Pablo Daniel Farace
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Claudia A Tortone
- Cátedra de Bacteriología y Micología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Pampa, General Pico, La Pampa, Argentina.
| | - Delia S Oriani
- Cátedra de Bacteriología y Micología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Pampa, General Pico, La Pampa, Argentina.
| | - Gianluca Picariello
- Istituto di Scienze Dell'Alimentazione, Consiglio Nazionale Delle Ricerche, Via Roma 64, 83100, Avellino, Italy.
| | - Martín José Zumárraga
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Andrea Karina Gioffré
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Paola M Talia
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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2
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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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Retuerto-Guerrero M, López-Medrano R, de Freitas-González E, Rivero-Lezcano OM. Nontuberculous Mycobacteria, Mucociliary Clearance, and Bronchiectasis. Microorganisms 2024; 12:665. [PMID: 38674609 PMCID: PMC11052484 DOI: 10.3390/microorganisms12040665] [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: 02/10/2024] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Nontuberculous mycobacteria (NTM) are environmental and ubiquitous, but only a few species are associated with disease, often presented as nodular/bronchiectatic or cavitary pulmonary forms. Bronchiectasis, airways dilatations characterized by chronic productive cough, is the main presentation of NTM pulmonary disease. The current Cole's vicious circle model for bronchiectasis proposes that it progresses from a damaging insult, such as pneumonia, that affects the respiratory epithelium and compromises mucociliary clearance mechanisms, allowing microorganisms to colonize the airways. An important bronchiectasis risk factor is primary ciliary dyskinesia, but other ciliopathies, such as those associated with connective tissue diseases, also seem to facilitate bronchiectasis, as may occur in Lady Windermere syndrome, caused by M. avium infection. Inhaled NTM may become part of the lung microbiome. If the dose is too large, they may grow excessively as a biofilm and lead to disease. The incidence of NTM pulmonary disease has increased in the last two decades, which may have influenced the parallel increase in bronchiectasis incidence. We propose that ciliary dyskinesia is the main promoter of bronchiectasis, and that the bacteria most frequently involved are NTM. Restoration of ciliary function and impairment of mycobacterial biofilm formation may provide effective therapeutic alternatives to antibiotics.
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Affiliation(s)
- Miriam Retuerto-Guerrero
- Servicio de Reumatología, Complejo Asistencial Universitario de León, Gerencia Regional de Salud de Castilla y León (SACYL), Altos de Nava, s/n, 24071 León, Spain;
| | - Ramiro López-Medrano
- Servicio de Microbiología Clínica, Complejo Asistencial Universitario de León, Gerencia Regional de Salud de Castilla y León (SACYL), Altos de Nava, s/n, 24071 León, Spain;
| | - Elizabeth de Freitas-González
- Servicio de Neumología, Complejo Asistencial Universitario de León, Gerencia Regional de Salud de Castilla y León (SACYL), Altos de Nava, s/n, 24071 León, Spain;
| | - Octavio Miguel Rivero-Lezcano
- Unidad de Investigación, Complejo Asistencial Universitario de León, Gerencia Regional de Salud de Castilla y León (SACYL), Altos de Nava, s/n, 24071 León, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Institute of Biomedicine (IBIOMED), University of León, 24071 León, Spain
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4
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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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5
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Schmalstig AA, Wiggins A, Badillo D, Wetzel KS, Hatfull GF, Braunstein M. Bacteriophage infection and killing of intracellular Mycobacterium abscessus. mBio 2024; 15:e0292423. [PMID: 38059609 PMCID: PMC10790704 DOI: 10.1128/mbio.02924-23] [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: 11/05/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023] Open
Abstract
IMPORTANCE As we rapidly approach a post-antibiotic era, bacteriophage (phage) therapy may offer a solution for treating drug-resistant bacteria. Mycobacterium abscessus is an emerging, multidrug-resistant pathogen that causes disease in people with cystic fibrosis, chronic obstructive pulmonary disease, and other underlying lung diseases. M. abscessus can survive inside host cells, a niche that can limit access to antibiotics. As current treatment options for M. abscessus infections often fail, there is an urgent need for alternative therapies. Phage therapy is being used to treat M. abscessus infections as an option of last resort. However, little is known about the ability of phages to kill bacteria in the host environment and specifically in an intracellular environment. Here, we demonstrate the ability of phages to enter mammalian cells and to infect and kill intracellular M. abscessus. These findings support the use of phages to treat intracellular bacterial pathogens.
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Affiliation(s)
- Alan A. Schmalstig
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Andrew Wiggins
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Debbie Badillo
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katherine S. Wetzel
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Miriam Braunstein
- Department of Microbiology and Immunology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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6
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Jessu A, Delafont V, Moyen JL, Biet F, Samba-Louaka A, Héchard Y. Characterization of Rosculus vilicus sp. nov., a rhizarian amoeba interacting with Mycobacterium avium subsp. paratuberculosis. Front Microbiol 2023; 14:1324985. [PMID: 38188567 PMCID: PMC10770858 DOI: 10.3389/fmicb.2023.1324985] [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: 10/20/2023] [Accepted: 12/06/2023] [Indexed: 01/09/2024] Open
Abstract
Free-living amoebae are described as potential reservoirs for pathogenic bacteria in the environment. It has been hypothesized that this might be the case for Mycobacterium avium subsp. paratuberculosis, the bacterium responsible for paratuberculosis. In a previous work, we isolated an amoeba from a water sample in the environment of infected cattle and showed that this amoeba was associated with Mycobacterium avium subsp. paratuberculosis. While a partial 18S rRNA gene has allowed us to suggest that this amoeba was Rosculus-like, at that time we were not able to sub-cultivate it. In the present study, we succeeded in cultivating this strain at 20-25°C. This amoeba is among the smallest (5-7 μm) described. The sequencing of the whole genome allowed us to extract the full 18S rRNA gene and propose this strain as a new species of the Rosculus genus, i.e., R. vilicus. Of note, the mitochondrial genome is particularly large (184,954 bp). Finally, we showed that this amoeba was able to phagocyte Mycobacterium avium subsp. paratuberculosis and that the bacterium was still observed within amoebae after at least 3 days. In conclusion, we characterized a new environmental amoeba species at the cellular and genome level that was able to interact with Mycobacterium avium subsp. paratuberculosis. As a result, R. vilicus is a potential candidate as environmental reservoir for Mycobacterium avium subsp. paratuberculosis but further experiments are needed to test this hypothesis.
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Affiliation(s)
- Amélie Jessu
- Université de Poitiers, CNRS, EBI, Poitiers, France
- Laboratoire Départemental d’Analyse et de Recherche de la Dordogne, Coulounieix-Chamiers, France
| | | | - Jean-Louis Moyen
- Laboratoire Départemental d’Analyse et de Recherche de la Dordogne, Coulounieix-Chamiers, France
| | - Franck Biet
- Laboratoire Départemental d’Analyse et de Recherche de la Dordogne, Coulounieix-Chamiers, France
| | | | - Yann Héchard
- Université de Poitiers, CNRS, EBI, Poitiers, France
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7
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Cinicola BL, Ottaviano G, Hashim IF, Zainudeen ZT, Hamid IJA, Elfeky R. Prevalence and Characteristics of Non-tuberculous Mycobacteria (NTM) Infection in Recipients of Allogeneic Hematopoietic Stem Cell Transplantation: a Systematic Review and Meta-analysis. J Clin Immunol 2023; 44:23. [PMID: 38129624 PMCID: PMC10739425 DOI: 10.1007/s10875-023-01615-3] [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: 07/31/2023] [Accepted: 10/22/2023] [Indexed: 12/23/2023]
Abstract
PURPOSE Non-tuberculous mycobacteria (NTM) infections in hematopoietic stem cell transplantation (HSCT) recipients represent a diagnostic and therapeutic challenge. Here, we aimed to review and analyze current literature on incidence, clinical presentation, and outcome of NTM infection after allogeneic HSCT. METHODS We performed a systematic review and meta-analysis of available literature regarding NTM infection in children and adults receiving allogeneic HSCT. RESULTS We identified 56 articles eligible for the analysis. Among 15 studies, describing 15,798 allogeneic HSCT, we estimated a prevalence of 1.26% (95% CI 0.72, 1.93) of NTM after transplant. Analysis of 175 patients with NTM infection showed a median time of diagnosis of 318 days after HSCT, an increased prevalence in adults (82.9%), and a most frequent pulmonary involvement (44%). Comparison between children and adults revealed an earlier post-transplant disease onset (median 130 days vs 287 days) and most frequent non-pulmonary presentation in children. A vast heterogeneity of therapeutic approach reflected the lack of universal recommendations regarding drug combination and duration of therapy. Overall, NTM-related mortality accounted for 33% in this systematic review. CONCLUSION Although rare, NTM infections can complicate post-transplant course with a high mortality rate in children and adults. The lack of prospective studies and guidelines prevents identification of risk factors and therapeutic recommendations.
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Affiliation(s)
- Bianca Laura Cinicola
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Rome, Italy
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Giorgio Ottaviano
- Department of Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Ilie Fadzilah Hashim
- Primary Immunodeficiency Diseases Group, Department of Clinical Medicine, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Zarina Thasneem Zainudeen
- Primary Immunodeficiency Diseases Group, Department of Clinical Medicine, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Intan Juliana Abd Hamid
- Primary Immunodeficiency Diseases Group, Department of Clinical Medicine, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Pulau Pinang, Malaysia.
| | - Reem Elfeky
- Department of Immunology, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London, UK.
- GOS Hospital for Children NHS Foundation Trust, University College London GOS Institute of Child Health, and NIHR GOSH BRC, London, UK.
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8
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Pis Diez CM, Antelo GT, Dalia TN, Dalia AB, Giedroc DP, Capdevila DA. Increased intracellular persulfide levels attenuate HlyU-mediated hemolysin transcriptional activation in Vibrio cholerae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532278. [PMID: 36993174 PMCID: PMC10054925 DOI: 10.1101/2023.03.13.532278] [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] [Indexed: 06/19/2023]
Abstract
The vertebrate host’s immune system and resident commensal bacteria deploy a range of highly reactive small molecules that provide a barrier against infections by microbial pathogens. Gut pathogens, such as Vibrio cholerae , sense and respond to these stressors by modulating the expression of exotoxins that are crucial for colonization. Here, we employ mass-spectrometry-based profiling, metabolomics, expression assays and biophysical approaches to show that transcriptional activation of the hemolysin gene hlyA in V. cholerae is regulated by intracellular reactive sulfur species (RSS), specifically sulfane sulfur. We first present a comprehensive sequence similarity network analysis of the arsenic repressor (ArsR) superfamily of transcriptional regulators where RSS and reactive oxygen species (ROS) sensors segregate into distinct clusters. We show that HlyU, transcriptional activator of hlyA in V. cholerae , belongs to the RSS-sensing cluster and readily reacts with organic persulfides, showing no reactivity and remaining DNA-bound following treatment with various ROS in vitro, including H 2 O 2 . Surprisingly, in V. cholerae cell cultures, both sulfide and peroxide treatment downregulate HlyU-dependent transcriptional activation of hlyA . However, RSS metabolite profiling shows that both sulfide and peroxide treatment raise the endogenous inorganic sulfide and disulfide levels to a similar extent, accounting for this crosstalk, and confirming that V. cholerae attenuates HlyU-mediated activation of hlyA in a specific response to intracellular RSS. These findings provide new evidence that gut pathogens may harness RSS-sensing as an evolutionary adaptation that allows them to overcome the gut inflammatory response by modulating the expression of exotoxins.
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Affiliation(s)
- Cristian M. Pis Diez
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de, Buenos Aires, Argentina
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Giuliano T. Antelo
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de, Buenos Aires, Argentina
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Triana N. Dalia
- Department of Biology, Indiana University, Bloomington, IN 47405-7102, USA
| | - Ankur B. Dalia
- Department of Biology, Indiana University, Bloomington, IN 47405-7102, USA
| | - David P. Giedroc
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA
| | - Daiana A. Capdevila
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA-CONICET), C1405BWE Ciudad Autónoma de, Buenos Aires, Argentina
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9
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Raymond CM, Nielsen MC, Silva C, Tanabe M, Clement C, Williams-Bouyer N, He J. Vacuoles in the Breast: A Histologic Clue for an Unusual Presentation of an Atypical Organism. Cureus 2023; 15:e36586. [PMID: 37095826 PMCID: PMC10122441 DOI: 10.7759/cureus.36586] [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] [Accepted: 03/23/2023] [Indexed: 04/26/2023] Open
Abstract
Infections with nontuberculous mycobacteria (NTM) are increasing in prevalence worldwide, and this group of organisms is emerging as significant clinical pathogens. We present a case of a 58-year-old female with persistent furuncles of the breast who was found to have an NTM infection. This case is unique for the lack of risk factors for NTM in the patient's history, the location of the infection in the breast, and the close cooperation needed across disciplines to arrive at the diagnosis. This multi-disciplinary discussion considers the classic clinical presentation of NTM, it is a characteristic morphological appearance on histopathology, the differential diagnosis, treatment, and the ultimate outcome of the case. This case report and discussion will assist both clinicians and pathologists in the diagnosis of this important infectious disease.
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Affiliation(s)
- Caitlin M Raymond
- Pathology, University of Texas Medical Branch at Galveston, Galveston, USA
| | - Marisa C Nielsen
- Pathology and Laboratory Medicine, Boston Medical Center, Boston, USA
| | - Colleen Silva
- Surgery, University of Texas Medical Branch at Galveston, Galveston, USA
| | - Melinda Tanabe
- Infectious Disease, University of Texas Medical Branch at Galveston, Galveston, USA
| | - Cecilia Clement
- Pathology, University of Texas Medical Branch at Galveston, Galveston, USA
| | | | - Jing He
- Pathology, University of Texas Medical Branch at Galveston, Galveston, USA
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10
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Pepperell CS. Evolution of Tuberculosis Pathogenesis. Annu Rev Microbiol 2022; 76:661-680. [PMID: 35709500 DOI: 10.1146/annurev-micro-121321-093031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mycobacterium tuberculosis is a globally distributed, lethal pathogen of humans. The virulence armamentarium of M. tuberculosis appears to have been developed on a scaffold of antiphagocytic defenses found among diverse, mostly free-living species of Mycobacterium. Pathoadaptation was further aided by the modularity, flexibility, and interactivity characterizing mycobacterial effectors and their regulators. During emergence of M. tuberculosis, novel genetic material was acquired, created, and integrated with existing tools. The major mutational mechanisms underlying these adaptations are discussed in this review, with examples. During its evolution, M. tuberculosis lost the ability and/or opportunity to engage in lateral gene transfer, but despite this it has retained the adaptability that characterizes mycobacteria. M. tuberculosis exemplifies the evolutionary genomic mechanisms underlying adoption of the pathogenic niche, and studies of its evolution have uncovered a rich array of discoveries about how new pathogens are made. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Caitlin S Pepperell
- Division of Infectious Diseases, Department of Medicine, and Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA;
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11
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Wakeman W, Long A, Estes AM, Jozwick AKS. Zebrafish, Danio rerio, Skin Mucus Harbors a Distinct Bacterial Community Dominated by Actinobacteria. Zebrafish 2021; 18:354-362. [PMID: 34935499 DOI: 10.1089/zeb.2021.0040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The skin mucus of teleost fish harbors a complex microbial community that is continually interacting with the aquatic environment. Despite zebrafish, Danio rerio, serving as a model organism in a myriad of research fields, very little is known about the composition and role of the skin mucus microbiome. The purpose of this study was to determine a simple sampling method for the skin mucus microbiome, identify prominent bacterial members, and compare its composition to the microbial community of the surrounding environment. Next-generation sequencing of the V3-V4 region of the 16S rRNA gene was performed on skin mucus and filtered tank water samples. Results show that prominent bacterial members of the skin mucus in zebrafish include Actinobacteria (Mycobacteriaceae) and Gammaproteobacteria (Aeromonadaceae), followed by Alphaproteobacteria and Betaproteobacteria. The tank water contained much higher bacterial diversity and was clearly different from the skin mucus microbiome, despite continuous interaction. This study identifies a straightforward sampling method for the zebrafish skin mucus microbiome, enabling hypothesis generation on the role of ectosymbionts on host and microbiome health.
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Affiliation(s)
- Wren Wakeman
- Center for Natural Sciences, Goucher College, Baltimore, Maryland, USA
| | - Alyssa Long
- Center for Natural Sciences, Goucher College, Baltimore, Maryland, USA
| | - Anne M Estes
- Department of Biological Sciences, Towson University, Baltimore, Maryland, USA
| | - Anna K S Jozwick
- Center for Natural Sciences, Goucher College, Baltimore, Maryland, USA
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12
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Wastewater-Based Surveillance of Antibiotic Resistance Genes Associated with Tuberculosis Treatment Regimen in KwaZulu Natal, South Africa. Antibiotics (Basel) 2021; 10:antibiotics10111362. [PMID: 34827300 PMCID: PMC8614817 DOI: 10.3390/antibiotics10111362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
Essential components of public health include strengthening the surveillance of infectious diseases and developing early detection and prevention policies. This is particularly important for drug-resistant tuberculosis (DR-TB), which can be explored by using wastewater-based surveillance. This study aimed to use molecular techniques to determine the occurrence and concentration of antibiotic-resistance genes (ARGs) associated with tuberculosis (TB) resistance in untreated and treated wastewater. Raw/untreated and treated (post-chlorination) wastewater samples were taken from three wastewater treatment plants (WWTPs) in South Africa. The ARGs were selected to target drugs used for first- and second-line TB treatment. Both conventional polymerase chain reaction (PCR) and the more advanced droplet digital PCR (ddPCR) were evaluated as surveillance strategies to determine the distribution and concentration of the selected ARGs. The most abundant ARG in the untreated wastewater was the rrs gene, associated with resistance to the aminoglycosides, specifically streptomycin, with median concentration ranges of 4.69–5.19 log copies/mL. In contrast, pncA gene, associated with resistance to the TB drug pyrazinamide, was the least detected (1.59 to 2.27 log copies/mL). Resistance genes associated with bedaquiline was detected, which is a significant finding because this is a new drug introduced in South Africa for the treatment of multi-drug resistant TB. This study, therefore, establishes the potential of molecular surveillance of wastewater for monitoring antibiotic resistance to TB treatment in communities.
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13
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Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition. mSystems 2021; 6:e0119421. [PMID: 34665012 PMCID: PMC8525567 DOI: 10.1128/msystems.01194-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nontuberculous mycobacteria, including those in the Mycobacterium avium complex (MAC), constitute an increasingly urgent threat to global public health. Ubiquitous in soil and water worldwide, MAC members cause a diverse array of infections in humans and animals that are often multidrug resistant, intractable, and deadly. MAC lung disease is of particular concern and is now more prevalent than tuberculosis in many countries, including the United States. Although the clinical importance of these microorganisms continues to expand, our understanding of their genomic diversity is limited, hampering basic and translational studies alike. Here, we leveraged a unique collection of genomes to characterize MAC population structure, gene content, and within-host strain dynamics in unprecedented detail. We found that different MAC species encode distinct suites of biomedically relevant genes, including antibiotic resistance genes and virulence factors, which may influence their distinct clinical manifestations. We observed that M. avium isolates from different sources—human pulmonary infections, human disseminated infections, animals, and natural environments—are readily distinguished by their core and accessory genomes, by their patterns of horizontal gene transfer, and by numerous specific genes, including virulence factors. We identified highly similar MAC strains from distinct patients within and across two geographically distinct clinical cohorts, providing important insights into the reservoirs which seed community acquisition. We also discovered a novel MAC genomospecies in one of these cohorts. Collectively, our results provide key genomic context for these emerging pathogens and will facilitate future exploration of MAC ecology, evolution, and pathogenesis. IMPORTANCE Members of the Mycobacterium avium complex (MAC), a group of mycobacteria encompassing M. avium and its closest relatives, are omnipresent in natural environments and emerging pathogens of humans and animals. MAC infections are difficult to treat, sometimes fatal, and increasingly common. Here, we used comparative genomics to illuminate key aspects of MAC biology. We found that different MAC species and M. avium isolates from different sources encode distinct suites of clinically relevant genes, including those for virulence and antibiotic resistance. We identified highly similar MAC strains in patients from different states and decades, suggesting community acquisition from dispersed and stable reservoirs, and we discovered a novel MAC species. Our work provides valuable insight into the genomic features underlying these versatile pathogens.
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14
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Interaction Patterns between Wildlife and Cattle Reveal Opportunities for Mycobacteria Transmission in Farms from North-Eastern Atlantic Iberian Peninsula. Animals (Basel) 2021; 11:ani11082364. [PMID: 34438821 PMCID: PMC8388635 DOI: 10.3390/ani11082364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/31/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Interactions taking place between sympatric wildlife and livestock may contribute to interspecies transmission of the Mycobacterium tuberculosis complex or non-tuberculous mycobacteria, leading to the spread of relevant mycobacterioses or to interferences with the diagnosis of tuberculosis. The aim of this study was to characterize the spatiotemporal patterns of interactions between wildlife and cattle in a low bovine tuberculosis prevalence Atlantic region. Camera traps were set during a one-year period in cattle farms with a history of tuberculosis and/or non-tuberculous mycobacterioses. The frequency and duration of wildlife visits, and the number of individuals per visit, were analysed through generalized linear mixed models. The seasons, type of place, type of point, and period of the day were the explanatory variables. A total of 1293 visits were recorded during 2741 days of camera observation. Only 23 visits showed direct contacts with cattle, suggesting that mycobacteria transmission at the wildlife-livestock interface would occur mainly through indirect interactions. Cattle pastures represented the most appropriate habitat for interspecies transmission of mycobacteria, and badgers' latrines appear to be a potential hotspot for mycobacteria circulation between badgers, wild boars, foxes, and cattle. According to both previous epidemiological information and the interaction patterns observed, wild boars, badgers, foxes, and small rodents are the species or group most often in contact with livestock, and thus may be the most involved in the epidemiology of mycobacterioses in the wildlife-livestock interface in this area.
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15
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Chalmers JD, van Ingen J, van der Laan R, Herrmann JL. Liposomal drug delivery to manage nontuberculous mycobacterial pulmonary disease and other chronic lung infections. Eur Respir Rev 2021; 30:30/161/210010. [PMID: 34289985 PMCID: PMC9488898 DOI: 10.1183/16000617.0010-2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/01/2021] [Indexed: 12/20/2022] Open
Abstract
Nontuberculous mycobacterial (NTM) pulmonary disease is a chronic respiratory infection associated with declining lung function, radiological deterioration and significantly increased morbidity and mortality. Patients often have underlying lung conditions, particularly bronchiectasis and COPD. NTM pulmonary disease is difficult to treat because mycobacteria can evade host defences and antimicrobial therapy through extracellular persistence in biofilms and sequestration into macrophages. Management of NTM pulmonary disease remains challenging and outcomes are often poor, partly due to limited penetration of antibiotics into intracellular spaces and biofilms. Efficient drug delivery to the site of infection is therefore a key objective of treatment, but there is high variability in lung penetration by antibiotics. Inhalation is the most direct route of delivery and has demonstrated increased efficacy of antibiotics like amikacin compared with systemic administration. Liposomes are small, artificial, enclosed spherical vesicles, in which drug molecules can be encapsulated to provide controlled release, with potentially improved pharmacokinetics and reduced toxicity. They are especially useful for drugs where penetration of cell membranes is essential. Inhaled delivery of liposomal drug solutions can therefore facilitate direct access to macrophages in the lung where the infecting NTM may reside. A range of liposomal drugs are currently being evaluated in respiratory diseases. Liposome-encapsulated antibiotics can optimise respiratory disease treatment. Amikacin liposomal inhalation suspension is effective in nontuberculous mycobacterial pulmonary disease that has failed to convert following oral guideline-based therapy.https://bit.ly/3f3ixIu
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Affiliation(s)
- James D Chalmers
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Jakko van Ingen
- Dept of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Jean-Louis Herrmann
- Université Paris-Saclay, UVSQ, INSERM, Infection and Inflammation, Montigny-le-Bretonneux, France.,APHP, Groupe Hospitalo-Universitaire Paris-Saclay, Hôpital Raymond Poincaré, Garches, France
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16
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Zulu M, Monde N, Nkhoma P, Malama S, Munyeme M. Nontuberculous Mycobacteria in Humans, Animals, and Water in Zambia: A Systematic Review. FRONTIERS IN TROPICAL DISEASES 2021. [DOI: 10.3389/fitd.2021.679501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) are environmental opportunistic pathogens of humans and animals that are emerging with a serious public health impact particularly in individuals with Acquired Immunodeficiency Syndromes. Recent scientific evidence is shifting from NTMs being known as traditional environmental organisms to serious pathogenic organisms in both animals and humans. In humans, factors attributable to this rise have been linked mainly to Human Immunodeficiency Virus and Acquired Immunodeficiency Syndrome pandemic. In recent years there has been an increase in multidrug resistant Tuberculosis in Zambia and it is thought that NTMs could possibly be the cause. This study was therefore formulated to review available information on the prevalence of NTM in humans, animals and the environment, species distribution, zoonotic potential and public health importance in Zambia. This review was conducted in accordance with PRISMA guidelines. A literature search was done in PubMed and Google scholar using predefined search terms such as ‘nontuberculous mycobacteria’, ‘atypical mycobacteria’, ‘mycobacteria other than mycobacterium tuberculosis’ and ‘Zambia’, in combination with Boolean operators (AND, OR). This particular systematic review draws findings based on literature search between 2000 and 2020. Through literature search 243 papers were identified, 23 duplicates were identified and removed and 206 articles were excluded as they did not meet the inclusion criteria. The full text of the remaining 14 articles were considered for this review. The overall prevalence of NTM in humans was 24.39%, in water 21.5%, in animals 16.05% of which the prevalence in cattle was 14.81% and Kafue Lechwe 1.23%. Mycobacterium intracellulare was the most common isolated nontuberculous mycobacteria in humans and cattle while Mycobacterium gordonae was the most common in water, and Mycobacterium stomatepiae sp Nov in Kafue Lechwe. Nontuberculous mycobacteria are an emerging public health threat in Zambia both in humans and animals and this calls for the need for molecular information on the zoonotic transmission of nontuberculous mycobacteria. Increased awareness of nontuberculous mycobacteria diseases among clinicians and laboratory personnel is crucial for patient management and an essential step for facilitating the identification of nontuberculous mycobacteria species in laboratories.
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17
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Guo J, Ning XQ, Ding JY, Zheng YQ, Shi NN, Wu FY, Lin YK, Shih HP, Ting HT, Liang G, Lu XC, Kong JL, Wang K, Lu YB, Fu YJ, Hu R, Li TM, Pan KS, Li XY, Huang CY, Lo YF, Chang IYF, Yeh CF, Tu KH, Tsai YH, Ku CL, Cao CW. Anti-IFN-γ autoantibodies underlie disseminated Talaromyces marneffei infections. J Exp Med 2021; 217:152070. [PMID: 32880631 PMCID: PMC7953730 DOI: 10.1084/jem.20190502] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/22/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
Talaromyces marneffei causes life-threatening opportunistic infections, mainly in Southeast Asia and South China. T. marneffei mainly infects patients with human immunodeficiency virus (HIV) but also infects individuals without known immunosuppression. Here we investigated the involvement of anti-IFN-γ autoantibodies in severe T. marneffei infections in HIV-negative patients. We enrolled 58 HIV-negative adults with severe T. marneffei infections who were otherwise healthy. We found a high prevalence of neutralizing anti-IFN-γ autoantibodies (94.8%) in this cohort. The presence of anti-IFN-γ autoantibodies was strongly associated with HLA-DRB1*16:02 and -DQB1*05:02 alleles in these patients. We demonstrated that adult-onset acquired immunodeficiency due to autoantibodies against IFN-γ is the major cause of severe T. marneffei infections in HIV-negative patients in regions where this fungus is endemic. The high prevalence of anti-IFN-γ autoantibody-associated HLA class II DRB1*16:02 and DQB1*05:02 alleles may account for severe T. marneffei infections in Southeast Asia. Our findings clarify the pathogenesis of T. marneffei infection and pave the way for developing novel treatments.
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Affiliation(s)
- Jing Guo
- Department of Dermatology and Venereology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xin-Qiang Ning
- Department of Dermatology and Venereology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Jing-Ya Ding
- Laboratory of Human Immunology and Infectious Disease, Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Yan-Qing Zheng
- Department of Dermatology and Venereology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Fourth People's Hospital of Nanning, Nanning, Guangxi, China
| | - Na-Na Shi
- Department of Dermatology and Venereology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Feng-Yao Wu
- Fourth People's Hospital of Nanning, Nanning, Guangxi, China
| | - You-Kun Lin
- Department of Dermatology and Venereology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Han-Po Shih
- Laboratory of Human Immunology and Infectious Disease, Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - He-Ting Ting
- Laboratory of Human Immunology and Infectious Disease, Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Gang Liang
- School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiang-Chan Lu
- Fourth People's Hospital of Nanning, Nanning, Guangxi, China
| | - Jin-Ling Kong
- Department of Respiratory Medicine, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Ke Wang
- School of Preclinical Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Yi-Bo Lu
- Fourth People's Hospital of Nanning, Nanning, Guangxi, China
| | - Yu-Jiao Fu
- Department of Dermatology and Venereology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Rong Hu
- Department of Dermatology and Venereology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Tian-Min Li
- Department of Dermatology and Venereology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Kai-Su Pan
- Department of Dermatology and Venereology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiu-Ying Li
- Department of Dermatology and Venereology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Chun-Yang Huang
- Department of Dermatology and Venereology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
| | - Yu-Fang Lo
- Laboratory of Human Immunology and Infectious Disease, Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Ian Yi-Feng Chang
- Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chun-Fu Yeh
- Laboratory of Human Immunology and Infectious Disease, Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan.,Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kun-Hua Tu
- Laboratory of Human Immunology and Infectious Disease, Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan.,Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Huan Tsai
- Laboratory of Host-Microbe Interactions and Cell Dynamics, Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan
| | - Cheng-Lung Ku
- Laboratory of Human Immunology and Infectious Disease, Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan.,Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Graduate Institute of Clinical Medical Science, China Medical University, Taichung, Taiwan
| | - Cun-Wei Cao
- Department of Dermatology and Venereology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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18
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Identification of Nontuberculous Mycobacteria in Patients with Pulmonary Diseases in Gyeongnam, Korea, Using Multiplex PCR and Multigene Sequence-Based Analysis. ACTA ACUST UNITED AC 2021; 2021:8844306. [PMID: 33688383 PMCID: PMC7920741 DOI: 10.1155/2021/8844306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/27/2021] [Accepted: 02/08/2021] [Indexed: 11/18/2022]
Abstract
Background Nontuberculous mycobacteria (NTM) are widely present in environments, such as soil and water, and have recently been recognized as important pathogenic bacteria. The incidence of NTM-related infections is steadily increasing. As the diagnosis and treatment of NTM infection should be distinguished from tuberculosis, and the treatment should be specific to the species of NTM acquired, accurate species identification is required. Methods In this study, two-step multiplex PCR (mPCR) and multigene sequence-based analysis were used to accurately identify NTM species in 320 clinical isolates from Gyeongsang National University Hospital (GNUH). In particular, major mycobacterial strains with a high isolation frequency as well as coinfections with multiple species were diagnosed through two-step mPCR. Multigene sequencing was performed to accurately identify other NTM species not detected by mPCR. Variable regions of the genes 16S rRNA, rpoB, hsp65, and 16S-23S rRNA internal transcribed spacer were included in the analysis. Results Two-step mPCR identified 234 (73.1%) cases of M. intracellulare, 26 (8.1%) cases of M. avium subsp. avium, and 13 (4.1%) cases of M. avium subsp. hominissuis infection. Additionally, 9 (2.8%) M. fortuitum, 9 (2.8%) M. massiliense, 2 (0.6%) M. abscessus, and 4 (1.2%) M. kansasii isolates were identified. Coinfection was identified in 7 (2.2%) samples. The sixteen samples not classified by two-step mPCR included 6 (1.9%) cases of M. chimaera, 4 (1.3%) M. gordonae, 1 (0.3%) M. colombiense, 1 (0.3%) M. mageritense, and 1 (0.3%) M. persicum identified by sequence analysis. Conclusions The results of this study suggest a strategy for rapid detection and accurate identification of species using two-step mPCR and multigene sequence-based analysis. To the best of our knowledge, this study is the first to report the identification of NTM species isolated from patients in Gyeongnam/Korea.
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Ali ZI, Hanafy M, Hansen C, Saudi AM, Talaat AM. Genotypic analysis of nontuberculous mycobacteria isolated from raw milk and human cases in Wisconsin. J Dairy Sci 2020; 104:211-220. [PMID: 33162087 DOI: 10.3168/jds.2020-18214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 08/17/2020] [Indexed: 11/19/2022]
Abstract
Nontuberculous mycobacteria (NTM) compose a group of mycobacteria that do not belong to the Mycobacterium tuberculosis complex group. They are frequently isolated from environmental samples such as water, soil, and, to a lesser extent, food samples. Isolates of NTM represent a major health threat to humans worldwide, especially those who have asthma or are immunocompromised. Human disease is acquired from environmental exposures and through consumption of NTM-contaminated food. The most common clinical manifestation of NTM disease in human is lung disease, but lymphatic, skin and soft tissue, and disseminated disease are also important. The main objective of the current study was to profile the farm-level contamination of cow milk with NTM by examining milk filters and bulk tank milk samples. Five different NTM species were isolated in one dairy herd in Wisconsin, with confirmed 16S rRNA genotypes including Mycobacterium fortuitum, Mycobacterium avium ssp. hominissuis, Mycobacterium abscessus, Mycobacterium simiae, and Mycobacterium avium ssp. paratuberculosis (Mycobacterium paratuberculosis). In tank milk samples, M. fortuitum was the predominant species in 48% of the samples, whereas M. chelonae/abscessus and M. fortuitum were the only 2 species obtained from 77 and 23% of the examined filters, respectively. Surprisingly, M. avium ssp. hominissuis, M. paratuberculosis, and M. simiae were isolated from 16.7, 10.4, and 4% of the examined milk samples, respectively, but not from milk filters. Interestingly, NTM isolates from human clinical cases in Wisconsin clustered very closely with those from milk samples. These findings suggest that the problem of NTM contamination is underestimated in dairy herds and could contribute to human infections with NTM. Overall, the study validates the use of bulk tank samples rather than milk filters to assess contamination of milk with NTM. Nontuberculous mycobacteria represent one type of pathogens that extensively contaminate raw milk at the farm level. The significance of our research is in evaluating the existence of NTM at the farm level and identifying a simple approach to examine the potential milk contamination with NTM members using tank milk or milk filters from dairy operations. In addition, we attempted to examine the potential link between NTM isolates found in the farm to those circulating in humans in Wisconsin.
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Affiliation(s)
- Zeinab I Ali
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Mostafa Hanafy
- Department of Pathobiological Sciences, University of Wisconsin, Madison 53706; Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Chungyi Hansen
- Department of Pathobiological Sciences, University of Wisconsin, Madison 53706
| | - Adel M Saudi
- Department of Food Hygiene and Control, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Adel M Talaat
- Department of Pathobiological Sciences, University of Wisconsin, Madison 53706.
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20
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Weeks JW, Segars K, Guha S. The Research Gap in Non-tuberculous Mycobacterium (NTM) and Reusable Medical Devices. Front Public Health 2020; 8:399. [PMID: 32974254 PMCID: PMC7468515 DOI: 10.3389/fpubh.2020.00399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/07/2020] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jon W Weeks
- Center for Devices and Radiological Health, U. S. Food and Drug Administration, Silver Spring, MD, United States
| | - Katharine Segars
- Center for Devices and Radiological Health, U. S. Food and Drug Administration, Silver Spring, MD, United States
| | - Suvajyoti Guha
- Center for Devices and Radiological Health, U. S. Food and Drug Administration, Silver Spring, MD, United States
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21
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Madani A, Mallick I, Guy A, Crauste C, Durand T, Fourquet P, Audebert S, Camoin L, Canaan S, Cavalier JF. Dissecting the antibacterial activity of oxadiazolone-core derivatives against Mycobacterium abscessus. PLoS One 2020; 15:e0238178. [PMID: 32946441 PMCID: PMC7500638 DOI: 10.1371/journal.pone.0238178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 08/12/2020] [Indexed: 02/05/2023] Open
Abstract
Mycobacterium abscessus (M. abscessus), a rapidly growing mycobacterium, is an emergent opportunistic pathogen responsible for chronic bronchopulmonary infections in individuals with respiratory diseases such as cystic fibrosis. Most treatments of M. abscessus pulmonary infections are poorly effective due to the intrinsic resistance of this bacteria against a broad range of antibiotics including anti-tuberculosis agents. Consequently, the number of drugs that are efficient against M. abscessus remains limited. In this context, 19 oxadiazolone (OX) derivatives have been investigated for their antibacterial activity against both the rough (R) and smooth (S) variants of M. abscessus. Several OXs impair extracellular M. abscessus growth with moderated minimal inhibitory concentrations (MIC), or act intracellularly by inhibiting M. abscessus growth inside infected macrophages with MIC values similar to those of imipenem. Such promising results prompted us to identify the potential target enzymes of the sole extra and intracellular inhibitor of M. abscessus growth, i.e., compound iBpPPOX, via activity-based protein profiling combined with mass spectrometry. This approach led to the identification of 21 potential protein candidates being mostly involved in M. abscessus lipid metabolism and/or in cell wall biosynthesis. Among them, the Ag85C protein has been confirmed as a vulnerable target of iBpPPOX. This study clearly emphasizes the potential of the OX derivatives to inhibit the extracellular and/or intracellular growth of M. abscessus by targeting various enzymes potentially involved in many physiological processes of this most drug-resistant mycobacterial species.
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Affiliation(s)
- Abdeldjalil Madani
- Aix-Marseille Univ., CNRS, LISM, Institut de Microbiologie de la Méditerranée FR3479, Marseille, France
| | - Ivy Mallick
- Aix-Marseille Univ., CNRS, LISM, Institut de Microbiologie de la Méditerranée FR3479, Marseille, France
- IHU Méditerranée Infection, Aix-Marseille Univ., Marseille, France
| | - Alexandre Guy
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Céline Crauste
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Thierry Durand
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Patrick Fourquet
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Stéphane Audebert
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Luc Camoin
- Aix-Marseille Univ, INSERM, CNRS, Institut Paoli-Calmettes, CRCM, Marseille Protéomique, Marseille, France
| | - Stéphane Canaan
- Aix-Marseille Univ., CNRS, LISM, Institut de Microbiologie de la Méditerranée FR3479, Marseille, France
| | - Jean François Cavalier
- Aix-Marseille Univ., CNRS, LISM, Institut de Microbiologie de la Méditerranée FR3479, Marseille, France
- * E-mail:
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22
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de Carvalho CCCR, Teixeira R, Fernandes P. Mycobacterium vaccae Adaptation to Disinfectants and Hand Sanitisers, and Evaluation of Cross-Tolerance with Antimicrobials. Antibiotics (Basel) 2020; 9:antibiotics9090544. [PMID: 32867093 PMCID: PMC7559525 DOI: 10.3390/antibiotics9090544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium vaccae is being considered as an adjuvant to antituberculosis therapy, tested for the treatment of autoimmune diseases, and as an anti-depressive agent. This bacterium is ubiquitous in the environment and the widespread use of disinfectants and sanitisers may lead to its adaptation to these compounds. In the present study, M. vaccae cells adapted to these compounds mainly by making adjustments in their lipid composition and net surface charge. The modifications in the lipid composition led to changes in membrane permeability which resulted in increased tolerance towards levofloxacin, thioridazine, and omeprazole.
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Affiliation(s)
- Carla C. C. R. de Carvalho
- Department of Bioengineering, iBB–Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (R.T.); (P.F.)
- Correspondence: ; Tel.: +351-21-841-9594
| | - Raquel Teixeira
- Department of Bioengineering, iBB–Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (R.T.); (P.F.)
| | - Pedro Fernandes
- Department of Bioengineering, iBB–Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; (R.T.); (P.F.)
- DREAMS and Faculty of Engineering, Universidade Lusófona de Humanidades e Tecnologias, 1749-024 Lisbon, Portugal
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23
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Ohji R, Shinohara T, Ohji H, Hatakeyama N, Iwamura S, Ogushi F. Pulmonary tuberculosis misdiagnosed as extensively drug-resistant tuberculosis due to selection of a nontuberculous mycobacterial colony from a preculture dish used for a drug-susceptibility test. Respir Investig 2020; 58:216-219. [PMID: 32131991 DOI: 10.1016/j.resinv.2019.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/07/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Drug-susceptibility test (DST) is important for tuberculosis care; however, there are several pitfalls with the procedure. A 70-year-old woman was diagnosed with extensively drug-resistant tuberculosis based on the result of a DST using microdilution method. Because she had no history of medication for tuberculosis and the sputum acid-fast bacillus smear test turned negative during standard treatment, identification of the strain used for DST was performed. Consequently, the strain was found to be M. intracellulare. It was assumed that a colony of M. intracellulare that had existed in the preculture solid medium was selected and used for the DST.
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Affiliation(s)
- Reina Ohji
- Division of Pulmonary Medicine, National Hospital Organization Kochi Hospital, 1-2-25 Asakuranishimachi, Kochi 780-8077, Japan.
| | - Tsutomu Shinohara
- Department of Clinical Investigation, National Hospital Organization Kochi Hospital, 1-2-25 Asakuranishimachi, Kochi 780-8077, Japan; Department of Community Medicine for Respirology, Graduate School of Biomedical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan.
| | - Hiroshi Ohji
- Division of Pulmonary Medicine, National Hospital Organization Kochi Hospital, 1-2-25 Asakuranishimachi, Kochi 780-8077, Japan.
| | - Nobuo Hatakeyama
- Division of Pulmonary Medicine, National Hospital Organization Kochi Hospital, 1-2-25 Asakuranishimachi, Kochi 780-8077, Japan.
| | - Sachiko Iwamura
- Division of Clinical Laboratory, National Hospital Organization Kochi Hospital, 1-2-25 Asakuranishimachi, Kochi 780-8077, Japan.
| | - Fumitaka Ogushi
- Division of Pulmonary Medicine, National Hospital Organization Kochi Hospital, 1-2-25 Asakuranishimachi, Kochi 780-8077, Japan.
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24
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de Ruyck J, Dupont C, Lamy E, Le Moigne V, Biot C, Guérardel Y, Herrmann J, Blaise M, Grassin‐Delyle S, Kremer L, Dubar F. Structure-Based Design and Synthesis of Piperidinol-Containing Molecules as New Mycobacterium abscessus Inhibitors. ChemistryOpen 2020; 9:351-365. [PMID: 32211280 PMCID: PMC7083170 DOI: 10.1002/open.202000042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Indexed: 02/06/2023] Open
Abstract
Non-tuberculous mycobacterium (NTM) infections, such as those caused by Mycobacterium abscessus, are increasing globally. Due to their intrinsic drug resistance, M. abscessus pulmonary infections are often difficult to cure using standard chemotherapy. We previously demonstrated that a piperidinol derivative, named PIPD1, is an efficient molecule both against M. abscessus and Mycobacterium tuberculosis, the agent of tuberculosis, by targeting the mycolic acid transporter MmpL3. These results prompted us to design and synthesize a series of piperidinol derivatives and to determine the biological activity against M. abscessus. Structure-activity relationship (SAR) studies pointed toward specific sites on the scaffold that can tolerate slight modifications. Overall, these results identified FMD-88 as a new promising active analogue against M. abscessus. Also, we determined the pharmacokinetics properties of PIPD1 and showed that intraperitoneal administration of this compound resulted in promising serum concentration and an elimination half-life of 3.2 hours.
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Affiliation(s)
- Jérôme de Ruyck
- Univ. Lille, CNRS UMR 8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle59000LilleFrance
| | - Christian Dupont
- IRIM Institut de Recherche en Infectiologie de Montpellier – UMR9004-CNRS/UM1919 route de Mende34293MontpellierFrance
| | - Elodie Lamy
- Infection et inflammation – Laboratoire 2I UMD1173-INSERM/UVSQVersailles2 Avenue de la source de la Bièvres78180Montigny le BretonneuxFrance
| | - Vincent Le Moigne
- Infection et inflammation – Laboratoire 2I UMD1173-INSERM/UVSQVersailles2 Avenue de la source de la Bièvres78180Montigny le BretonneuxFrance
| | - Christophe Biot
- Univ. Lille, CNRS UMR 8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle59000LilleFrance
| | - Yann Guérardel
- Univ. Lille, CNRS UMR 8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle59000LilleFrance
| | - Jean‐Louis Herrmann
- Infection et inflammation – Laboratoire 2I UMD1173-INSERM/UVSQVersailles2 Avenue de la source de la Bièvres78180Montigny le BretonneuxFrance
- Université Paris-Saclay, UVSQ, INSERMInfection et Inflammation (U1173)Montigny le BretonneuxFrance
| | - Mickaël Blaise
- IRIM Institut de Recherche en Infectiologie de Montpellier – UMR9004-CNRS/UM1919 route de Mende34293MontpellierFrance
| | - Stanislas Grassin‐Delyle
- Infection et inflammation – Laboratoire 2I UMD1173-INSERM/UVSQVersailles2 Avenue de la source de la Bièvres78180Montigny le BretonneuxFrance
- Hôpital FochDépartement des maladies des voies respiratoires92150SuresnesFrance
| | - Laurent Kremer
- IRIM Institut de Recherche en Infectiologie de Montpellier – UMR9004-CNRS/UM1919 route de Mende34293MontpellierFrance
- INSERM, Institut de Recherche en Infectiologie de MontpellierMontpellierFrance
| | - Faustine Dubar
- Univ. Lille, CNRS UMR 8576 – UGSF – Unité de Glycobiologie Structurale et Fonctionnelle59000LilleFrance
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25
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Biofilms of Mycobacterium abscessus Complex Can Be Sensitized to Antibiotics by Disaggregation and Oxygenation. Antimicrob Agents Chemother 2020; 64:AAC.01212-19. [PMID: 31740557 DOI: 10.1128/aac.01212-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/03/2019] [Indexed: 12/25/2022] Open
Abstract
Pulmonary infection with the multidrug-resistant Mycobacterium abscessus complex (MABSC) is difficult to treat in individuals with cystic fibrosis (CF). MABSC grows as biofilm aggregates in CF patient lungs, which are known to have anaerobic niches. How aggregation and anoxic conditions affect antibiotic tolerance is not well understood. We sought to determine whether disaggregation and oxygen availability sensitize MABSC isolates to recommended antibiotics. We tested the susceptibilities of 33 isolates from 22 CF patients with MABSC infection and a reference strain to the following antibiotics: amikacin, azithromycin, cefoxitin, ciprofloxacin, clarithromycin, imipenem, kanamycin, linezolid, moxifloxacin, rifampin, tigecycline, and sulfamethoxazole-trimethoprim. Isolates were grown in Mueller-Hinton broth with and without the disaggregating detergent Tween 80 (5%). Time-kill curves at days 1 and 3 were generated for oxic and anoxic amikacin treatment in 4-fold dilutions ranging from 2 to 512 mg liter-1 Scanning electron microscopy was used to visualize the aggregation patterns, while confocal laser scanning microscopy and microrespirometry were used to visualize biofilm growth patterns. Disruption of MABSC aggregates increased susceptibility to amikacin, tigecycline, kanamycin, azithromycin, imipenem, cefoxitin, and clarithromycin (P < 0.05, n = 29 to 31). Oxygenation enhanced the killing of disaggregated MABSC isolates by amikacin (P < 0.05) by 1 to 6 log units when 2 to 512 mg liter-1 of amikacin was used. This study explains why current drug susceptibility testing results correlate poorly with treatment outcomes. The conditions achieved by oxic culturing of planktonic isolates in vitro do not resemble the hypoxic conditions in CF patient lungs. Biofilm disruption and increased O2 availability during antibiotic therapy may be new therapeutic strategies for chronic MABSC infection.
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26
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Bouso JM, Planet PJ. Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing. BMC Genomics 2019; 20:793. [PMID: 31666009 PMCID: PMC6822416 DOI: 10.1186/s12864-019-6134-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Background Nontuberculous mycobacteria (NTM) are a major cause of pulmonary and systemic disease in at-risk populations. Gaps in knowledge about transmission patterns, evolution, and pathogenicity during infection have prompted a recent surge in genomic NTM research. Increased availability and affordability of whole genome sequencing (WGS) techniques provide new opportunities to sequence and construct complete bacterial genomes faster and at a lower cost. However, extracting large quantities of pure genomic DNA is particularly challenging with NTM due to its slow growth and recalcitrant cell wall. Here we report a DNA extraction protocol that is optimized for long-read WGS of NTM, yielding large quantities of highly pure DNA with no additional clean-up steps. Results Our DNA extraction method was compared to 6 other methods with variations in timing of mechanical disruption and enzymatic digestion of the cell wall, quantity of matrix material, and reagents used in extraction and precipitation. We tested our optimized method on 38 clinical isolates from the M. avium and M. abscessus complexes, which yielded optimal quality and quantity measurements for Oxford Nanopore Technologies sequencing. We also present the efficient completion of circularized M. avium subspecies hominissuis genomes using our extraction technique and the long-read sequencing MinION platform, including the identification of a novel plasmid. Conclusions Our optimized extraction protocol and assembly pipeline was both sufficient and efficient for genome closure. We expect that our finely-tuned extraction method will prove to be a valuable tool in long-read sequencing and completion of mycobacterial genomes going forward. Utilization of comprehensive, long-read based approaches will advance the understanding evolution and pathogenicity of NTM infections.
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Affiliation(s)
- Jennifer M Bouso
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul J Planet
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
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27
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Claeys TA, Rosas Mejia O, Marshall S, Jarzembowski JA, Hayes D, Hull NM, Liyanage NPM, Chun RH, Sulman CG, Huppler AR, Robinson RT. Attenuation of Helper T Cell Capacity for TH1 and TH17 Differentiation in Children With Nontuberculous Mycobacterial Infection. J Infect Dis 2019; 220:1843-1847. [PMID: 31332447 DOI: 10.1093/infdis/jiz371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/17/2019] [Indexed: 12/19/2022] Open
Abstract
Nontuberculous mycobacteria (NTM) infect children with increasing frequency worldwide. Using blood and lymph node tissue from children with NTM lymphadenitis, and uninfected lymph node tissue from community controls, we evaluated helper T (TH) cells in functional assays of TH1/TH17 differentiation and measured the concentration of their associated cytokines at the site of infection. Circulating TH cells from infected children were attenuated in their TH1/TH17 differentiation capacity and expressed less interferon γ and interleukin 17 after polyclonal stimulation. Similar differences were observed at the site of infection, where most cytokine concentrations were unchanged relative to controls. Our data are consistent with a model wherein TH1/TH17 differentiation is attenuated in NTM-infected children.
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Affiliation(s)
- Tiffany A Claeys
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus
| | - Oscar Rosas Mejia
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus
| | - Samuel Marshall
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee
| | - Jason A Jarzembowski
- Department of Pathology, Medical College of Wisconsin, Medical College of Wisconsin, Milwaukee
| | - Don Hayes
- Department of Pediatrics, Nationwide Children's Hospital and The Ohio State University College of Medicine, Columbus
| | - Natalie M Hull
- Department of Civil, Environmental, and Architectural Engineering, The Ohio State University, Columbus
| | - Namal P M Liyanage
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus
| | - Robert H Chun
- Division of Pediatric Otolaryngology, Department of Surgery, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee
| | - Cecille G Sulman
- Division of Pediatric Otolaryngology, Department of Surgery, Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee
| | - Anna R Huppler
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee.,Division of Infectious Disease, Department of Pediatrics, Medical College of Wisconsin and Children's Hospital and Health System, Children's Research Institute, Milwaukee
| | - Richard T Robinson
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus
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Socio-Economic and Environmental Factors Related to Spatial Differences in Human Non-Tuberculous Mycobacterial Diseases in the Czech Republic. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16203969. [PMID: 31627484 PMCID: PMC6843547 DOI: 10.3390/ijerph16203969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/16/2019] [Indexed: 02/07/2023]
Abstract
Non-tuberculous mycobacteria (NTM) are ubiquitous environmental bacteria that can induce pulmonary and non-pulmonary diseases in susceptible persons. It is reported that the prevalence of NTM diseases is increasing in developed countries, but this differs by regions and countries. NTM species distribution and the rate of diseases caused by NTM vary widely in the historical territories of Moravia and Silesia (Czech Republic). This epidemiologic study of NTM diseases covers the period 2012–2018, reviews isolates obtained from patients with clinical disease and investigates correlations with related socio-economic and environmental factors. Individual NTM patients were included only once during the studied period and results were presented as incidence rate per year. The most frequently isolated NTM meeting the microbiological and clinical criteria in the study were the Mycobacterium avium-intracellulare complex, followed by Mycobacterium kansasii and Mycobacteriumxenopi. A previously described endemic incidence of M.kansasii in the Karviná district and M.xenopi in the Ostrava district was also observed in this study. The incidence of NTM patients in the whole studied territory was 1.10/100,000 inhabitants (1.33/100,000 in men and 0.88/100,000 in women). The annual incidence of lymphadenitis in children (≤5 years of age) was 2.35/100,000 of the population of children during the 7 year period but increased in the year 2018 to 5.95/100,000. The rate of human tuberculosis in the studied area was 1.97/100,000 inhabitants. The incidence of NTM pulmonary diseases correlated with a lower socio-economic status (r = 0.63) and a higher concentration of benzo[a]pyrene pollution in the air (r = 0.64).
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29
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Is the Potable Water System an Advantageous Preinfection Niche for Bacteria Colonizing the Cystic Fibrosis Lung? mBio 2019; 10:mBio.00883-19. [PMID: 31164466 PMCID: PMC6550525 DOI: 10.1128/mbio.00883-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
People with cystic fibrosis are susceptible to lung infections from a variety of bacteria, a number of which also reside in the potable water system, including Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Burkholderia cepacia complex, and nontuberculosis Mycobacteria. Here, I propose chemical and physical aspects of the potable water system along with bacterial lifestyle strategies in this system that may enhance successful colonization of cystic fibrosis lungs by these bacteria, including iron and copper levels, lipids, and low growth rates within low-oxygen biofilms. People with cystic fibrosis are susceptible to lung infections from a variety of bacteria, a number of which also reside in the potable water system, including Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Burkholderia cepacia complex, and nontuberculosis Mycobacteria. Here, I propose chemical and physical aspects of the potable water system along with bacterial lifestyle strategies in this system that may enhance successful colonization of cystic fibrosis lungs by these bacteria, including iron and copper levels, lipids, and low growth rates within low-oxygen biofilms.
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30
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Franch O, Han X, Marcussen LB, Givskov A, Andersen MB, Godbole AA, Harmsen C, Nørskov-Lauritsen N, Thomsen J, Pedersen FS, Wang Y, Shi D, Wejse C, Pødenphant L, Nagaraja V, Bertl J, Stougaard M, Ho YP, Hede MS, Labouriau R, Knudsen BR. A new DNA sensor system for specific and quantitative detection of mycobacteria. NANOSCALE 2019; 11:587-597. [PMID: 30556557 DOI: 10.1039/c8nr07850e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the current study, we describe a novel DNA sensor system for specific and quantitative detection of mycobacteria, which is the causative agent of tuberculosis. Detection is achieved by using the enzymatic activity of the mycobacterial encoded enzyme topoisomerase IA (TOP1A) as a biomarker. The presented work is the first to describe how the catalytic activities of a member of the type IA family of topoisomerases can be exploited for specific detection of bacteria. The principle for detection relies on a solid support anchored DNA substrate with dual functions namely: (1) the ability to isolate mycobacterial TOP1A from crude samples and (2) the ability to be converted into a closed DNA circle upon reaction with the isolated enzyme. The DNA circle can act as a template for rolling circle amplification generating a tandem repeat product that can be visualized at the single molecule level by fluorescent labelling. This reaction scheme ensures specific, sensitive, and quantitative detection of the mycobacteria TOP1A biomarker as demonstrated by the use of purified mycobacterial TOP1A and extracts from an array of non-mycobacteria and mycobacteria species. When combined with mycobacteriophage induced lysis as a novel way of effective yet gentle extraction of the cellular content from the model Mycobacterium smegmatis, the DNA sensor system allowed detection of mycobacteria in small volumes of cell suspensions. Moreover, it was possible to detect M. smegmatis added to human saliva. Depending on the composition of the sample, we were able to detect 0.6 or 0.9 million colony forming units (CFU) per mL of mycobacteria, which is within the range of clinically relevant infection numbers. We, therefore, believe that the presented assay, which relies on techniques that can be adapted to limited resource settings, may be the first step towards the development of a new point-of-care diagnostic test for tuberculosis.
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Affiliation(s)
- Oskar Franch
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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31
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Wood HN, Sidders AE, Brumsey LE, Morozkin ES, Gerasimova YV, Rohde KH. Species Typing of Nontuberculous Mycobacteria by Use of Deoxyribozyme Sensors. Clin Chem 2018; 65:333-341. [PMID: 30523201 DOI: 10.1373/clinchem.2018.295212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/15/2018] [Indexed: 01/16/2023]
Abstract
BACKGROUND Nontuberculous mycobacteria (NTM) species are a rising threat, especially to patients living with pulmonary comorbidities. Current point-of-care diagnostics fail to adequately identify and differentiate NTM species from Mycobacterium tuberculosis (Mtb). Definitive culture- and molecular-based testing can take weeks to months and requires sending samples out to specialized diagnostic laboratories. METHODS In this proof-of-concept study, we developed an assay based on PCR amplification of 16S ribosomal RNA (rRNA) rrs genes by using universal mycobacterial primers and interrogation of the amplified fragments with a panel of binary deoxyribozyme (BiDz) sensors to enable species-level identification of NTM (BiDz-NTMST). Each BiDz sensor consists of 2 subunits of an RNA-cleaving deoxyribozyme, which form an active deoxyribozyme catalytic core only in the presence of the complimentary target sequence. The target-activated BiDz catalyzes cleavage of a reporter substrate, thus triggering either fluorescent or colorimetric (visually observed) signal depending on the substrate used. The panel included BiDz sensors for differentiation of 6 clinically relevant NTM species (Mycobacterium abscessus, Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium fortuitum, Mycobacterium kansasii, and Mycobacterium gordonae) and Mtb. RESULTS Using the fluorescent BiDz-NTMST assay, we successfully identified the species of 38 clinical isolates. In addition, a subset of strains was tested with visual BiDz sensors, providing proof-of-concept for species typing of NTM by the naked eye. CONCLUSIONS The BiDz-NTMST assay is a novel platform for rapid identification of NTM species. This method is highly specific and significantly faster than current tools and is easily adaptable for onsite diagnostic laboratories in hospitals or clinical laboratories.
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Affiliation(s)
- Hillary N Wood
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL
| | - Ashelyn E Sidders
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL
| | - Lauren E Brumsey
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL
| | - Evgeny S Morozkin
- Department of Chemistry, College of Sciences, University of Central Florida, Orlando, FL
| | - Yulia V Gerasimova
- Department of Chemistry, College of Sciences, University of Central Florida, Orlando, FL.
| | - Kyle H Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL;
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32
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De Groote MA, Jarvis TC, Wong C, Graham J, Hoang T, Young CL, Ribble W, Day J, Li W, Jackson M, Gonzalez-Juarrero M, Sun X, Ochsner UA. Optimization and Lead Selection of Benzothiazole Amide Analogs Toward a Novel Antimycobacterial Agent. Front Microbiol 2018; 9:2231. [PMID: 30294313 PMCID: PMC6158578 DOI: 10.3389/fmicb.2018.02231] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/31/2018] [Indexed: 12/14/2022] Open
Abstract
Mycobacteria remain an important problem worldwide, especially drug resistant human pathogens. Novel therapeutics are urgently needed to tackle both drug-resistant tuberculosis (TB) and difficult-to-treat infections with nontuberculous mycobacteria (NTM). Benzothiazole adamantyl amide had previously emerged as a high throughput screening hit against M. tuberculosis (Mtb) and was subsequently found to be active against NTM as well. For lead optimization, we applied an iterative process of design, synthesis and screening of several 100 analogs to improve antibacterial potency as well as physicochemical and pharmacological properties to ultimately achieve efficacy. Replacement of the adamantyl group with cyclohexyl derivatives, including bicyclic moieties, resulted in advanced lead compounds that showed excellent potency and a mycobacteria-specific spectrum of activity. MIC values ranged from 0.03 to 0.12 μg/mL against M. abscessus (Mabs) and other rapid- growing NTM, 1–2 μg/mL against M. avium complex (MAC), and 0.12–0.5 μg/mL against Mtb. No pre-existing resistance was found in a collection of n = 54 clinical isolates of rapid-growing NTM. Unlike many antibacterial agents commonly used to treat mycobacterial infections, benzothiazole amides demonstrated bactericidal effects against both Mtb and Mabs. Metabolic labeling provided evidence that the compounds affect the transfer of mycolic acids to their cell envelope acceptors in mycobacteria. Mapping of resistance mutations pointed to the trehalose monomycolate transporter (MmpL3) as the most likely target. In vivo efficacy and tolerability of a benzothiazole amide was demonstrated in a mouse model of chronic NTM lung infection with Mabs. Once daily dosing over 4 weeks by intrapulmonary microspray administration as 5% corn oil/saline emulsion achieved statistically significant CFU reductions compared to vehicle control and non-inferiority compared to azithromycin. The benzothiazole amides hold promise for development of a novel therapeutic agent with broad antimycobacterial activity, though further work is needed to develop drug formulations for direct intrapulmonary delivery via aerosol.
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Affiliation(s)
- Mary A De Groote
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | | | | | | | | | | | | | - Joshua Day
- Crestone, Inc., Boulder, CO, United States
| | - Wei Li
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Mercedes Gonzalez-Juarrero
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
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Blanco LP, Payne BL, Feyertag F, Alvarez-Ponce D. Proteins of generalist and specialist pathogens differ in their amino acid composition. Life Sci Alliance 2018; 1:e201800017. [PMID: 30456362 PMCID: PMC6238412 DOI: 10.26508/lsa.201800017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/25/2022] Open
Abstract
Pathogens differ in their host specificities, with species infecting a unique host (specialist pathogens) and others having a wide host range (generalists). Molecular determinants of pathogen's host range remain poorly understood. Secreted proteins of generalist pathogens are expected to have a broader range of intermolecular interactions (i.e., higher promiscuity) compared with their specialist counterparts. We hypothesize that this increased promiscuity of generalist secretomes may be based on an elevated content of primitive amino acids and intrinsically disordered regions, as these features are known to increase protein flexibility and interactivity. Here, we measure the proportion of primitive amino acids and percentage of intrinsically disordered residues in secreted, membrane, and cytoplasmic proteins from pathogens with different host specificity. Supporting our prediction, there is a significant general enrichment for primitive amino acids and intrinsically disordered regions in proteins from generalists compared to specialists, particularly among secreted proteins in prokaryotes. Our findings support our hypothesis that secreted proteins' amino acid composition and disordered content influence the pathogens' host range.
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Affiliation(s)
- Luz P Blanco
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bryan L Payne
- Department of Biology, University of Nevada, Reno, NV, USA
| | - Felix Feyertag
- Department of Biology, University of Nevada, Reno, NV, USA
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