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Das R, Nadar K, Arora R, Bajpai U. Unlocking prophage potential: In silico and experimental analysis of a novel Mycobacterium fortuitum LysinB containing a peptidoglycan-binding domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580446. [PMID: 38405724 PMCID: PMC10888907 DOI: 10.1101/2024.02.15.580446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Endolysins are highly evolved bacteriophage-encoded lytic enzymes produced to damage the bacterial cell wall for phage progeny release. They offer promising potential as highly specific lytic proteins with a low chance of bacterial resistance. The diversity in lysin sequences and domain organization can be staggering. In silico analysis of bacteriophage and prophage genomes can help identify endolysins exhibiting unique features and high antibacterial activity, hence feeding the pipeline of narrow-spectrum protein antibiotics. Mycobacteriophage lysis cassettes mostly have two lytic enzymes, LysinA and LysinB. The enzyme LysinA targets peptidoglycan in the cell wall and possesses a modular architecture. LysinB typically contains a single domain and acts upon the mycolyl ester linkages in mycolyl-arabinogalactan-peptidoglycan (Payne et al., 2010). This study aimed to find novel LysinBs against Mycobacterium fortuitum. After a detailed in silico characterization of lysis cassettes from three M. fortuitum prophages, we chose to work on a LysinB (hereafter described as LysinB_MF) found in an incomplete prophage (phiE1336, 9.4 kb in strain E1336). LysinB_MF showed low sequence similarity with any other endolysins in the database and formed a separate clade on phylogenetic analysis. LysinB_MF's structure, extracted from the AlphaFold Protein Structure Database, demonstrated a modular architecture with two structurally distinct domains: a peptidoglycan-binding domain (PGBD) at the N-terminal and the characteristic alpha/beta hydrolase domain connected via a linker peptide. We found the alpha/beta hydrolase domain, which is the enzyme-active domain (EAD), contains the conserved Ser-Asp-His catalytic triad with a tunnel-like topology and forms intermolecular hydrogen bonds. The PGBD shows structural similarity to the cell-wall binding domain of an amidase from Clostridium acetobutylicum, hinting at its acquisition due to domain mobility. Our in silico electrostatic potential analysis suggested that PGBD might be essential to the enzyme activity. This was experimentally validated by generating a truncated version of the enzyme, which demonstrated about six-fold decreased activity compared to its native form. The antimycobacterial activity of this enzyme was also compromised in its absence. Based on our analysis, PGBD emerged as an integral constituent of enzymes with diverse functional properties and is predicted to be a conserved cross-kingdom. Overall, this study highlights the importance of mining mycobacterial prophages as a novel endolysin source. It also provides unique insights into the diverse architecture of mycobacteriophage-encoded endolysins and the importance of functional domains for their catalytic activities.
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Affiliation(s)
- Ritam Das
- Faculty of Biological Sciences, Friedrich Schiller University, Jena-07737, Germany
- Department of Life Science, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji-110019, New Delhi, India
| | - Kanika Nadar
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji-110019, New Delhi, India
| | - Ritu Arora
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji-110019, New Delhi, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Govindpuri, Kalkaji-110019, New Delhi, India
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Howell AA, Versoza CJ, Cerna G, Johnston T, Kakde S, Karuku K, Kowal M, Monahan J, Murray J, Nguyen T, Sanchez Carreon A, Streiff A, Su B, Youkhana F, Munig S, Patel Z, So M, Sy M, Weiss S, Pfeifer SP. Phylogenomic analyses and host range prediction of cluster P mycobacteriophages. G3 (BETHESDA, MD.) 2022; 12:jkac244. [PMID: 36094333 PMCID: PMC9635641 DOI: 10.1093/g3journal/jkac244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Bacteriophages, infecting bacterial hosts in every environment on our planet, are a driver of adaptive evolution in bacterial communities. At the same time, the host range of many bacteriophages-and thus one of the selective pressures acting on complex microbial systems in nature-remains poorly characterized. Here, we computationally inferred the putative host ranges of 40 cluster P mycobacteriophages, including members from 6 subclusters (P1-P6). A series of comparative genomic analyses revealed that mycobacteriophages of subcluster P1 are restricted to the Mycobacterium genus, whereas mycobacteriophages of subclusters P2-P6 are likely also able to infect other genera, several of which are commonly associated with human disease. Further genomic analysis highlighted that the majority of cluster P mycobacteriophages harbor a conserved integration-dependent immunity system, hypothesized to be the ancestral state of a genetic switch that controls the shift between lytic and lysogenic life cycles-a temperate characteristic that impedes their usage in antibacterial applications.
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Affiliation(s)
| | | | - Gabriella Cerna
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Tyler Johnston
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Shriya Kakde
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Keith Karuku
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Maria Kowal
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jasmine Monahan
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jillian Murray
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Teresa Nguyen
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Aurely Sanchez Carreon
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Abigail Streiff
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Blake Su
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- School of Politics and Global Studies, Arizona State University, Tempe, AZ 85281, USA
| | - Faith Youkhana
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Saige Munig
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Zeel Patel
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Minerva So
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Makena Sy
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Sarah Weiss
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Susanne P Pfeifer
- Corresponding author: Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
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Pennington KM, Vu A, Challener D, Rivera CG, Shweta FNU, Zeuli JD, Temesgen Z. Approach to the diagnosis and treatment of non-tuberculous mycobacterial disease. J Clin Tuberc Other Mycobact Dis 2021; 24:100244. [PMID: 34036184 PMCID: PMC8135042 DOI: 10.1016/j.jctube.2021.100244] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Non-tuberculous mycobacteria (NTM) is a collective name given to a group of more than 190 species of Mycobacterium. The clinical presentation for most NTM infections is non-specific, often resulting in delayed diagnosis. Further complicating matters is that NTM organisms can be difficult to isolate. Medications used to treat NTM infection can be difficult for patients to tolerate, and prolonged courses of anti-mycobacterial therapy are often required for adequate suppression or eradication. Herein, we review different NTM syndromes, appropriate diagnostic tests, and treatment regimens.
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Key Words
- ADR, adverse drug reactions
- AFB, acid fast bacilli
- AST, antimicrobial-susceptibility testing
- ATS, American Thoracic Society
- BCG, Bacille Calmette-Guerin
- CLSI, Clinical and Laboratory Standards Institute
- COPD, chronic obstructive pulmonary disease
- ECG, electrocardiogram
- EMB, ethambutol
- Erm, erythromycin ribosomal methylase
- FDA, Food and Drug Administration
- HIV, human immunodeficiency virus
- HRCT, high resolution computed tomography
- IDSA, Infectious Disease Society of America
- INF-γ, interferon- γ
- INH, isoniazid
- MAC, Mycobacterium avium complex
- MALDI-TOF, matrix-assisted laser desorption ionization time-of-flight mass spectrometry
- MGIT, mycobacteria growth indicator tube
- MIC, minimum inhibitory concentrations
- Mycobacterium abscessus
- Mycobacterium avium
- NTM, non-tuberculous mycobacteria
- Non-tuberculous mycobacteria
- PCR, polymerase chain reaction
- PFT, pulmonary function test
- TB, tuberculosis
- TDM, therapeutic drug monitoring
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Affiliation(s)
- Kelly M Pennington
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic Rochester, MN, USA
| | - Ann Vu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Mayo Clinic Rochester, MN, USA
| | - Douglas Challener
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic Rochester, MN, USA
| | | | - F N U Shweta
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic Rochester, MN, USA
| | - John D Zeuli
- Department of Pharmacy, Mayo Clinic Rochester, MN, USA
| | - Zelalem Temesgen
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic Rochester, MN, USA
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Chin KL, Sarmiento ME, Alvarez-Cabrera N, Norazmi MN, Acosta A. Pulmonary non-tuberculous mycobacterial infections: current state and future management. Eur J Clin Microbiol Infect Dis 2020; 39:799-826. [PMID: 31853742 PMCID: PMC7222044 DOI: 10.1007/s10096-019-03771-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 11/18/2019] [Indexed: 12/11/2022]
Abstract
Currently, there is a trend of increasing incidence in pulmonary non-tuberculous mycobacterial infections (PNTM) together with a decrease in tuberculosis (TB) incidence, particularly in developed countries. The prevalence of PNTM in underdeveloped and developing countries remains unclear as there is still a lack of detection methods that could clearly diagnose PNTM applicable in these low-resource settings. Since non-tuberculous mycobacteria (NTM) are environmental pathogens, the vicinity favouring host-pathogen interactions is known as important predisposing factor for PNTM. The ongoing changes in world population, as well as socio-political and economic factors, are linked to the rise in the incidence of PNTM. Development is an important factor for the improvement of population well-being, but it has also been linked, in general, to detrimental environmental consequences, including the rise of emergent (usually neglected) infectious diseases, such as PNTM. The rise of neglected PNTM infections requires the expansion of the current efforts on the development of diagnostics, therapies and vaccines for mycobacterial diseases, which at present, are mainly focused on TB. This review discuss the current situation of PNTM and its predisposing factors, as well as the efforts and challenges for their control.
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Affiliation(s)
- Kai Ling Chin
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah (UMS), Kota Kinabalu, Sabah, Malaysia.
| | - Maria E Sarmiento
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia
| | - Nadine Alvarez-Cabrera
- Center for Discovery and Innovation (CDI), Hackensack Meridian School of Medicine at Seton Hall University, Nutley, NJ, USA
| | - Mohd Nor Norazmi
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia
| | - Armando Acosta
- School of Health Sciences, Universiti Sains Malaysia (USM), Kubang Kerian, Kelantan, Malaysia.
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da Silva Neto JP, Machado KNC, Roisman L. Choroidal granuloma caused by Mycobacterium Fortuitum. Int J Retina Vitreous 2019; 5:37. [PMID: 31636998 PMCID: PMC6791014 DOI: 10.1186/s40942-019-0185-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 08/12/2019] [Indexed: 11/29/2022] Open
Abstract
Background To report a case of a chronic steroid user male patient who developed local abscesses caused by M. fortuitum and concomitant asymptomatic choroidal granuloma. Case presentation A 37-year-old african-american male with history of use of anabolic drugs and intramuscular mineral oil injections in the upper and lower limbs for 15 years for muscular hypertrophy. He developed intramuscular abscesses with systemic infection, sub-retinal lesions in both eyes and alterations in cerebrospinal fluid suggestive of mycobacteria. Considering these findings, empirical treatment for tuberculosis was started, without success. After several negative cultures of the material drained from the abscesses, finally one of the cultures isolated the agent Mycobacterium Fortuitum. Proper treatment for atypical mycobacteria was initiated with clinical and laboratory improvement. After 6 months the sub-retinal lesions regressed. Conclusions A typical choroidal granuloma caused by M. Fortuitum is a rare presentation of the infection and our report showed a good outcome with proper treatment.
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Affiliation(s)
| | | | - Luiz Roisman
- Hospital Federal da Lagoa, Rio de Janeiro, Brazil.,2Federal University of São Paulo, São Paulo, Brazil
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Rapidly Growing Mycobacterial Infections of the Skin and Soft Tissues Caused by M. fortuitum and M. chelonae. CURRENT TROPICAL MEDICINE REPORTS 2018. [DOI: 10.1007/s40475-018-0150-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Entwistle FM, Coote PJ. Evaluation of greater wax moth larvae, Galleria mellonella, as a novel in vivo model for non-tuberculosis Mycobacteria infections and antibiotic treatments. J Med Microbiol 2018; 67:585-597. [PMID: 29458557 DOI: 10.1099/jmm.0.000696] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
PURPOSE To evaluate the suitability of Galleria mellonella larvae as an in vivo model and drug-screening tool for mycobacteria infections. METHODOLOGY Larvae were infected using a range of inoculum sizes from a variety of rapid-growing mycobacteria, including strains of M. fortuitum, M. marinum and M. aurum. Larval survival, internal bacterial burden and the effects of amikacin, ciprofloxacin, ethambutol, isoniazid and rifampicin treatment on larval survival were measured over 144 h. The effects of these anti-mycobacterial drugs on phagocytosis and circulating haemocyte numbers were also examined using microscopy. RESULTS Larval survival decreased after infection with M. fortuitum and M. marinum in a dose-dependent manner, but remained unaffected by M. aurum. Heat-killed bacteria did not cause larval death. Where antibiotic monotherapy was efficacious, larval survival post-infection increased in a dose-dependent fashion. However, efficacy varied between different antibiotics and species of infecting mycobacteria and, apart from rifampicin, efficacy in vivo correlated poorly with the in vitro minimum inhibitory concentrations (MICs). Combinations of antibiotics led to higher survival of infected larvae than antibiotic monotherapy. Selected antibiotic treatments that enhanced larval survival reduced the overall internal burden of infecting mycobacteria, but did not eradicate the pathogens. Administration of amikacin or ethambutol to uninfected larvae induced an initial transient increase in the numbers of circulating haemocytes and reduced the phagocytic rate of haemocytes in larvae infected with M. marinum. CONCLUSIONS This report demonstrates the potential of employing a wax moth larvae model for studying fast-growing mycobacteria infections, and as a cheap, effective system for initial screening of novel treatments.
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Affiliation(s)
- Frances M Entwistle
- Biomedical Sciences Research Complex, School of Biology, The North Haugh, University of St Andrews, Fife, KY16 9ST, UK
| | - Peter J Coote
- Biomedical Sciences Research Complex, School of Biology, The North Haugh, University of St Andrews, Fife, KY16 9ST, UK
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Ferzli GS, Thakkar P, Goldstein NA, Chernichenko N. Third Branchial Cleft Cyst with Mycobacterium Infection. OTO Open 2017; 1:2473974X17705832. [PMID: 30480182 PMCID: PMC6239023 DOI: 10.1177/2473974x17705832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/07/2017] [Accepted: 03/30/2017] [Indexed: 11/16/2022] Open
Affiliation(s)
- George S. Ferzli
- State University of New York Downstate Medical Center, Brooklyn, New York, USA
| | - Punam Thakkar
- State University of New York Downstate Medical Center, Brooklyn, New York, USA
| | - Nira A. Goldstein
- State University of New York Downstate Medical Center, Brooklyn, New York, USA
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Madhusudhan NS, Malini A, Sangma MMB. A Case of Surgical Site Infection Caused by Mycobacterium fortuitum, following Herniorrhaphy. J Clin Diagn Res 2017; 10:DD01-DD02. [PMID: 28050369 DOI: 10.7860/jcdr/2016/20045.8924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 08/13/2016] [Indexed: 11/24/2022]
Abstract
Rapidly Growing Mycobacteria (RGM) are opportunistic pathogens found in the environment. Mycobacterium fortuitum, M. chelonae and M.abscessus are the important human pathogens of this group. They cause wound infections, disseminated cutaneous disease, pulmonary infection in patients with cystic fibrosis or bronchiectasis, bone and joint infections and keratitis. Infections due to these Non-Tuberculous Mycobacteria (NTM) are increasingly reported. Post laparoscopic wound infections, mesh site infections and other surgical site infections due to M. fortuitum and M. chelonae have been reported. Usually wound infections due to atypical mycobacteria have delayed onset and do not respond to conventional antibiotics. Identification of RGM can be done by a set of cumbersome biochemical tests, High Performance Liquid Chromatography (HPLC), molecular methods using DNA probes or by Polymerase Chain Reaction (PCR). We here report a case of post-herniorrhaphy wound infection due to M. fortuitum which was identified by molecular method (HAIN mycobacterial species system). This case report underscores the importance of examining Ziehl-Neelsen (ZN) stain of all exudates with sterile culture on day one for non fastidious bacteria. Timely identification can lead to prompt therapy of patients preventing further complications.
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Affiliation(s)
- N S Madhusudhan
- Assistant Professor, Department of Microbiology, Indira Gandhi Medical College and Research Institute , Puducherry, India
| | - A Malini
- Associate Professor, Department of Microbiology, Indira Gandhi Medical College and Research Institute , Puducherry, India
| | - Mima Maychet B Sangma
- Associate Professor, Department of General Surgery, Indira Gandhi Medical College and Research Institute , Puducherry, India
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