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Oluoch PO, Koh EI, Proulx MK, Reames CJ, Papavinasasundaram KG, Murphy KC, Zimmerman MD, Dartois V, Sassetti CM. Chemical genetic interactions elucidate pathways controlling tuberculosis antibiotic efficacy during infection. Proc Natl Acad Sci U S A 2025; 122:e2417525122. [PMID: 39993187 PMCID: PMC11892619 DOI: 10.1073/pnas.2417525122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Accepted: 01/10/2025] [Indexed: 02/26/2025] Open
Abstract
Successful tuberculosis therapy requires treatment with an unwieldy multidrug combination for several months. Thus, there is a growing need to identify novel genetic vulnerabilities that can be leveraged to develop new, more effective antitubercular drugs. Consequently, recent efforts to optimize tuberculosis (TB) therapy have exploited Mycobacterium tuberculosis (Mtb) chemical genetics to identify pathways influencing antibiotic efficacy, novel mechanisms of antibiotic action, and new targets for TB drug discovery. However, the influence of the complex host environment on these interactions remains largely unknown, leaving the therapeutic potential of the identified targets unclear. In this study, we leveraged a library of conditional mutants targeting 467 essential Mtb genes to characterize the chemical-genetic interactions (CGIs) with TB drugs directly in the mouse infection model. We found that these in vivo CGIs differ significantly from those identified in vitro. Both drug-specific and drug-agnostic effects were identified, and many were preserved during treatment with a multidrug combination, suggesting numerous strategies for enhancing therapy. This work also elucidated the complex effects of pyrazinamide (PZA), a drug that relies on aspects of the infection environment for efficacy. Specifically, our work supports the importance of coenzyme A synthesis- inhibition during infection, as well as the antagonistic effect of iron limitation on PZA activity. In addition, we found that inhibition of thiamine and purine synthesis increases PZA efficacy, suggesting additional therapeutically exploitable metabolic dependencies. Our findings present a map of the unique in vivo CGIs, characterizing the mechanism of PZA activity in vivo and identifying potential targets for TB drug development.
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Affiliation(s)
- Peter O. Oluoch
- Department of Microbiology, University of Massachusetts Medical School, Worcester, MA01655
| | - Eun-Ik Koh
- Department of Microbiology, University of Massachusetts Medical School, Worcester, MA01655
| | - Megan K. Proulx
- Department of Microbiology, University of Massachusetts Medical School, Worcester, MA01655
| | - Charlotte J. Reames
- Department of Microbiology, University of Massachusetts Medical School, Worcester, MA01655
| | | | - Kenan C. Murphy
- Department of Microbiology, University of Massachusetts Medical School, Worcester, MA01655
| | - Matthew D. Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ07110
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ07110
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2
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Oluoch PO, Koh EI, Proulx MK, Reames CJ, Papavinasasundaram KG, Murphy KC, Zimmerman MD, Dartois V, Sassetti CM. Chemical genetic interactions elucidate pathways controlling tuberculosis antibiotic efficacy during infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.609063. [PMID: 39282290 PMCID: PMC11398305 DOI: 10.1101/2024.09.04.609063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2025]
Abstract
Successful tuberculosis therapy requires treatment with an unwieldy multidrug combination for several months. Thus, there is a growing need to identify novel genetic vulnerabilities that can be leveraged to develop new, more effective antitubercular drugs. Consequently, recent efforts to optimize TB therapy have exploited Mtb chemical genetics to identify pathways influencing antibiotic efficacy, novel mechanisms of antibiotic action, and new targets for TB drug discovery. However, the influence of the complex host environment on these interactions remains largely unknown, leaving the therapeutic potential of the identified targets unclear. In this study, we leveraged a library of conditional mutants targeting 467 essential Mtb genes to characterize the chemical-genetic interactions (CGIs) with TB drugs directly in the mouse infection model. We found that these in vivo CGIs differ significantly from those identified in vitro . Both drug-specific and drug-agnostic effects were identified, and many were preserved during treatment with a multidrug combination, suggesting numerous strategies for enhancing therapy. This work also elucidated the complex effects of pyrazinamide (PZA), a drug that relies on aspects of the infection environment for efficacy. Specifically, our work supports the importance of coenzyme A synthesis inhibition during infection, as well as the antagonistic effect of iron limitation on PZA activity. In addition, we found that inhibition of thiamine and purine synthesis increases PZA efficacy, suggesting novel therapeutically exploitable metabolic dependencies. Our findings present a map of the unique in vivo CGIs, characterizing the mechanism of PZA activity in vivo and identifying novel targets for TB drug development. Significance The inevitable rise of multi-drug-resistant tuberculosis underscores the urgent need for new TB drugs and novel drug targets while prioritizing synergistic drug combinations. Chemical-genetic interaction (CGI) studies have delineated bacterial pathways influencing antibiotic efficacy and uncovered druggable pathways that synergize with TB drugs. However, most studies are conducted in vitro , limiting our understanding of how the host environment influences drug-mutant interactions. Using an inducible mutant library targeting essential Mtb genes to characterize CGIs during infection, this study reveals that CGIs are both drug-specific and drug-agnostic and differ significantly from those observed in vitro . Synergistic CGIs comprised distinct metabolic pathways mediating antibiotic efficacy, revealing novel drug mechanisms of action, and defining potential drug targets that would synergize with frontline antitubercular drugs.
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3
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Li S, Poulton NC, Chang JS, Azadian ZA, DeJesus MA, Ruecker N, Zimmerman MD, Eckartt KA, Bosch B, Engelhart CA, Sullivan DF, Gengenbacher M, Dartois VA, Schnappinger D, Rock JM. CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis. Nat Microbiol 2022; 7:766-779. [PMID: 35637331 PMCID: PMC9159947 DOI: 10.1038/s41564-022-01130-y] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 04/21/2022] [Indexed: 12/14/2022]
Abstract
Mycobacterium tuberculosis (Mtb) infection is notoriously difficult to treat. Treatment efficacy is limited by Mtb's intrinsic drug resistance, as well as its ability to evolve acquired resistance to all antituberculars in clinical use. A deeper understanding of the bacterial pathways that influence drug efficacy could facilitate the development of more effective therapies, identify new mechanisms of acquired resistance, and reveal overlooked therapeutic opportunities. Here we developed a CRISPR interference chemical-genetics platform to titrate the expression of Mtb genes and quantify bacterial fitness in the presence of different drugs. We discovered diverse mechanisms of intrinsic drug resistance, unveiling hundreds of potential targets for synergistic drug combinations. Combining chemical genetics with comparative genomics of Mtb clinical isolates, we further identified several previously unknown mechanisms of acquired drug resistance, one of which is associated with a multidrug-resistant tuberculosis outbreak in South America. Lastly, we found that the intrinsic resistance factor whiB7 was inactivated in an entire Mtb sublineage endemic to Southeast Asia, presenting an opportunity to potentially repurpose the macrolide antibiotic clarithromycin to treat tuberculosis. This chemical-genetic map provides a rich resource to understand drug efficacy in Mtb and guide future tuberculosis drug development and treatment.
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Affiliation(s)
- Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Jesseon S Chang
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Zachary A Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Nadine Ruecker
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Matthew D Zimmerman
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Kathryn A Eckartt
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Daniel F Sullivan
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Martin Gengenbacher
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Hackensack Meridian Health, Nutley, NJ, USA
| | - Véronique A Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
- Hackensack Meridian School of Medicine, Hackensack Meridian Health, Nutley, NJ, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA.
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4
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Kaewprasert O, Tongsima S, Ong RTH, Faksri K. Optimized analysis parameters of variant calling for whole genome-based phylogeny of Mycobacteroides abscessus. Arch Microbiol 2022; 204:190. [PMID: 35194683 DOI: 10.1007/s00203-022-02792-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/17/2022] [Accepted: 02/04/2022] [Indexed: 02/05/2023]
Abstract
Whole-genome sequence (WGS) analysis provides the best resolution for reconstructing bacterial phylogeny. However, the resulting tree could vary according to parameters used in the WGS pipeline, making it difficult to compare results across multiple studies. This study compares effects on phylogenies when applying different parameter stringencies. We used as the study model to optimize parameters strains of Mycobacteroides abscessus serially isolated at various intervals, isolates known to represent persistent infection (PI) cases or re-infection (RI) cases and isolates from different subspecies. Un-optimized parameters with low stringency provided an excessive number of SNPs (823) compared to the optimized setting (3 SNPs) between paired strains isolated 1 day apart from PI cases, discordant tree topology and misclassification of subspecies and of instances of RI. We demonstrated that using high-quality variants provides more accuracy for recognizing serial isolates of the same clone versus different clones and for phylogenetic analysis of M. abscessus. Our approach might be used as a model for analyses requiring phylogenetic reconstruction of other bacteria.
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Affiliation(s)
- Orawee Kaewprasert
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
- National Center for Genetics Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani, Thailand
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand.
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
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5
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Remm S, Earp JC, Dick T, Dartois V, Seeger MA. Critical discussion on drug efflux in Mycobacterium tuberculosis. FEMS Microbiol Rev 2021; 46:6391500. [PMID: 34637511 PMCID: PMC8829022 DOI: 10.1093/femsre/fuab050] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/04/2021] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) can withstand months of antibiotic treatment. An important goal of tuberculosis research is to shorten the treatment to reduce the burden on patients, increase adherence to the drug regimen and thereby slow down the spread of drug resistance. Inhibition of drug efflux pumps by small molecules has been advocated as a promising strategy to attack persistent Mtb and shorten therapy. Although mycobacterial drug efflux pumps have been broadly investigated, mechanistic studies are scarce. In this critical review, we shed light on drug efflux in its larger mechanistic context by considering the intricate interplay between membrane transporters annotated as drug efflux pumps, membrane energetics, efflux inhibitors and cell wall biosynthesis processes. We conclude that a great wealth of data on mycobacterial transporters is insufficient to distinguish by what mechanism they contribute to drug resistance. Recent studies suggest that some drug efflux pumps transport structural lipids of the mycobacterial cell wall and that the action of certain drug efflux inhibitors involves dissipation of the proton motive force, thereby draining the energy source of all active membrane transporters. We propose recommendations on the generation and interpretation of drug efflux data to reduce ambiguities and promote assigning novel roles to mycobacterial membrane transporters.
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Affiliation(s)
- Sille Remm
- Institute of Medical Microbiology, University of Zürich, Switzerland
| | - Jennifer C Earp
- Institute of Medical Microbiology, University of Zürich, Switzerland
| | - Thomas Dick
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA.,Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA.,Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zürich, Switzerland
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6
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The ATP-Binding Cassette (ABC) Transport Systems in Mycobacterium tuberculosis: Structure, Function, and Possible Targets for Therapeutics. BIOLOGY 2020; 9:biology9120443. [PMID: 33291531 PMCID: PMC7761784 DOI: 10.3390/biology9120443] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 12/22/2022]
Abstract
Simple Summary Mycobacterium tuberculosis is a bacterium of great medical importance because it causes tuberculosis, a disease that affects millions of people worldwide. Two important features are related to this bacterium: its ability to infect and survive inside the host, minimizing the immune response, and the burden of clinical isolates that are highly resistant to antibiotics treatment. These two phenomena are directly affected by cell envelope proteins, such as proteins from the ATP-Binding Cassette (ABC transporters) superfamily. In this review, we have compiled information on all the M. tuberculosis ABC transporters described so far, both from a functional and structural point of view, and show their relevance for the bacillus and the potential targets for studies aiming to control the microorganism and structural features. Abstract Mycobacterium tuberculosis is the etiological agent of tuberculosis (TB), a disease that affects millions of people in the world and that is associated with several human diseases. The bacillus is highly adapted to infect and survive inside the host, mainly because of its cellular envelope plasticity, which can be modulated to adapt to an unfriendly host environment; to manipulate the host immune response; and to resist therapeutic treatment, increasing in this way the drug resistance of TB. The superfamily of ATP-Binding Cassette (ABC) transporters are integral membrane proteins that include both importers and exporters. Both types share a similar structural organization, yet only importers have a periplasmic substrate-binding domain, which is essential for substrate uptake and transport. ABC transporter-type importers play an important role in the bacillus physiology through the transport of several substrates that will interfere with nutrition, pathogenesis, and virulence. Equally relevant, exporters have been involved in cell detoxification, nutrient recycling, and antibiotics and drug efflux, largely affecting the survival and development of multiple drug-resistant strains. Here, we review known ABC transporters from M. tuberculosis, with particular focus on the diversity of their structural features and relevance in infection and drug resistance.
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Janubova M, Hatok J, Konarikova K, Zitnanova I. γ- and δ-Tocotrienols interfere with senescence leading to decreased viability of cells. Mol Cell Biochem 2020; 476:897-908. [PMID: 33128213 DOI: 10.1007/s11010-020-03954-w] [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: 07/03/2020] [Accepted: 10/15/2020] [Indexed: 11/30/2022]
Abstract
Senescence is an irreversible permanent cell cycle arrest accompanied by changes in cell morphology and physiology. Bioactive compounds including tocotrienols (vitamin E) can affect important biological functions. The aim of this study was to investigate how γ- and δ-tocotrienols can affect stress-induced premature senescence. We established two different models of premature stress senescence by induction of senescence with either hydrogen peroxide or etoposide in human lung fibroblasts MRC-5 (ECACC, England). We observed increased percentage of cells with increased SA-β-galactosidase activity, decreased cell viability/proliferation and increased level of p21 in both models. In addition, γ-tocotrienol or δ-tocotrienol (both at concentrations of 150, 200 and 300 μM) were added to the cells along with the inductor of senescence (cotreatment). We have found that this cotreatment led to the decrease of cell viability/proliferation in both models of premature stress senescence, but did not change the percentage of senescent cells. Moreover, we detected no expression of caspase-3 or apoptotic DNA fragmentation in any models of premature stress senescence after the cotreatment with γ- as well as δ-tocotrienols. However, an increased level of autophagic protein LC-3 II was detected in cells with hydrogen peroxide-induced senescence after the cotreatment with γ-tocotrienol as well as δ-tocotrienol. In case of etoposide-induced senescence only δ-tocotrienol cotreatment led to an increased level of LC-3 II protein in cells. According to our work δ-tocotrienol is more effective compound than γ-tocotrienol.
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Affiliation(s)
- Maria Janubova
- Faculty of Medicine, Institute of Medical Chemistry, Biochemistry and Clinical Biochemistry, Comenius University, Bratislava, Slovakia.
| | - Jozef Hatok
- Jessenius Faculty of Medicine, Department of Medical Biochemistry, Comenius University, Bratislava, Martin, Slovakia
| | - Katarina Konarikova
- Faculty of Medicine, Institute of Medical Chemistry, Biochemistry and Clinical Biochemistry, Comenius University, Bratislava, Slovakia
| | - Ingrid Zitnanova
- Faculty of Medicine, Institute of Medical Chemistry, Biochemistry and Clinical Biochemistry, Comenius University, Bratislava, Slovakia
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Tania T, Sudarmono P, Kusumawati RL, Rukmana A, Pratama WA, Regmi SM, Kaewprasert O, Chaiprasert A, Chongsuvivatwong V, Faksri K. Whole-genome sequencing analysis of multidrug-resistant Mycobacterium tuberculosis from Java, Indonesia. J Med Microbiol 2020; 69:1013-1019. [PMID: 32579102 DOI: 10.1099/jmm.0.001221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Multidrug-resistant tuberculosis (MDR-TB) is a major public health problem globally, including in Indonesia. Whole-genome sequencing (WGS) analysis has rarely been used for the study of TB and MDR-TB in Indonesia.Aim. We evaluated the use of WGS for drug-susceptibility testing (DST) and to investigate the population structure of drug-resistant Mycobacterium tuberculosis in Java, Indonesia.Methodology. Thirty suspected MDR-TB isolates were subjected to MGIT 960 system (MGIT)-based DST and to WGS. Phylogenetic analysis was done using the WGS data. Results obtained using MGIT-based DST and WGS-based DST were compared.Results. Agreement between WGS and MGIT was 93.33 % for rifampicin, 83.33 % for isoniazid and 76.67 % for streptomycin but only 63.33 % for ethambutol. Moderate WGS-MGIT agreement was found for second-line drugs including amikacin, kanamycin and fluoroquinolone (73.33-76.67 %). MDR-TB was more common in isolates of the East Asian Lineage (63.3%). No evidence of clonal transmission of DR-TB was found among members of the tested population.Conclusion. Our study demonstrated the applicability of WGS for DST and molecular epidemiology of DR-TB in Java, Indonesia. We found no transmission of DR-TB in Indonesia.
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Affiliation(s)
- Tryna Tania
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia-Cipto Mangunkusumo National Central General Hospital, Jakarta, Indonesia
| | - Pratiwi Sudarmono
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia-Cipto Mangunkusumo National Central General Hospital, Jakarta, Indonesia
| | - R Lia Kusumawati
- Department of Microbiology, Faculty of Medicine, Universitas Sumatera Utara-Adam Malik General Hospital, Medan, Indonesia
| | - Andriansjah Rukmana
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia-Cipto Mangunkusumo National Central General Hospital, Jakarta, Indonesia
| | - Wahyu Agung Pratama
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia-Cipto Mangunkusumo National Central General Hospital, Jakarta, Indonesia
| | - Sanjib Mani Regmi
- Department of Microbiology, Gandaki Medical College Teaching Hospital and Research Center, Pokhara, Nepal
| | - Orawee Kaewprasert
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Angkana Chaiprasert
- Office of Research Affairs, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
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Smith TC, Pullen KM, Olson MC, McNellis ME, Richardson I, Hu S, Larkins-Ford J, Wang X, Freundlich JS, Ando DM, Aldridge BB. Morphological profiling of tubercle bacilli identifies drug pathways of action. Proc Natl Acad Sci U S A 2020; 117:18744-18753. [PMID: 32680963 PMCID: PMC7414088 DOI: 10.1073/pnas.2002738117] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Morphological profiling is a method to classify target pathways of antibacterials based on how bacteria respond to treatment through changes to cellular shape and spatial organization. Here we utilized the cell-to-cell variation in morphological features of Mycobacterium tuberculosis bacilli to develop a rapid profiling platform called Morphological Evaluation and Understanding of Stress (MorphEUS). MorphEUS classified 94% of tested drugs correctly into broad categories according to modes of action previously identified in the literature. In the other 6%, MorphEUS pointed to key off-target activities. We observed cell wall damage induced by bedaquiline and moxifloxacin through secondary effects downstream from their main target pathways. We implemented MorphEUS to correctly classify three compounds in a blinded study and identified an off-target effect for one compound that was not readily apparent in previous studies. We anticipate that the ability of MorphEUS to rapidly identify pathways of drug action and the proximal cause of cellular damage in tubercle bacilli will make it applicable to other pathogens and cell types where morphological responses are subtle and heterogeneous.
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Affiliation(s)
- Trever C Smith
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
- Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA 02111
| | - Krista M Pullen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michaela C Olson
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
| | - Morgan E McNellis
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
| | - Ian Richardson
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
- Roxbury Latin School, West Roxbury, MA 02132
| | - Sophia Hu
- Department of Bioinformatics and Computational Biology, University of Maryland, Baltimore County, Baltimore, MD 21250
| | - Jonah Larkins-Ford
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111
- Tufts University School of Graduate Biomedical Sciences, Boston, MA 02111
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Xin Wang
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University-New Jersey Medical School, Newark, NJ 07103
| | - Joel S Freundlich
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University-New Jersey Medical School, Newark, NJ 07103
- Division of Infectious Disease, Department of Medicine, Rutgers University-New Jersey Medical School, Newark, NJ 07103
- Ruy V. Lourenco Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University-New Jersey Medical School, Newark, NJ 07103
| | - D Michael Ando
- Applied Science Team, Google Research, Mountain View, CA 94043
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111;
- Center for Integrated Management of Antimicrobial Resistance (CIMAR), Tufts University, Boston, MA 02111
- Tufts University School of Graduate Biomedical Sciences, Boston, MA 02111
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115
- Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA 02155
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10
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Chiu JKH, Ong RTH. ARGDIT: a validation and integration toolkit for Antimicrobial Resistance Gene Databases. Bioinformatics 2020; 35:2466-2474. [PMID: 30520940 DOI: 10.1093/bioinformatics/bty987] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/10/2018] [Accepted: 12/04/2018] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Antimicrobial resistance is currently one of the main challenges in public health due to the excessive use of antimicrobials in medical treatments and agriculture. The advancements in high-throughput next-generation sequencing and development of bioinformatics tools allow simultaneous detection and identification of antimicrobial resistance genes (ARGs) from clinical, food and environment samples, to monitor the prevalence and track the dissemination of these ARGs. Such analyses are however reliant on a comprehensive database of ARGs with accurate sequence content and annotation. Most of the current ARG databases are therefore manually curated, but this is a time-consuming process and the resulting curation errors could be hard to detect. Several secondary ARG databases consolidate contents from different source ARG databases, and hence modifications in the primary databases might not be propagated and updated promptly in the secondary ARG databases. RESULTS To address these problems, a validation and integration toolkit called ARGDIT was developed to validate ARG database fidelity, and merge multiple primary ARG databases into a single consolidated secondary ARG database with optional automated sequence re-annotation. Experimental results demonstrated the effectiveness of this toolkit in identifying errors such as sequence annotation typos in current ARG databases and generating an integrated non-redundant ARG database with structured annotation. A toolkit-oriented workflow is also proposed to minimize the efforts in validating, curating and merging multiple ARG protein or coding sequence databases. Database developers therefore benefit from faster update cycles and lower costs for database maintenance, while ARG pipeline users can easily evaluate the reference ARG database quality. AVAILABILITY AND IMPLEMENTATION ARGDIT is available at https://github.com/phglab/ARGDIT. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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11
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Ko KKK, Chio MTW, Goh SS, Tan AL, Koh TH, Abdul Rahman NB. First Case of Ceftriaxone-Resistant Multidrug-Resistant Neisseria gonorrhoeae in Singapore. Antimicrob Agents Chemother 2019; 63:e02624-18. [PMID: 30858209 PMCID: PMC6496044 DOI: 10.1128/aac.02624-18] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Karrie Kwan Ki Ko
- Department of Microbiology, Singapore General Hospital, Singapore
- Department of Molecular Pathology, Singapore General Hospital, Singapore
- Duke-NUS Graduate Medical School, Singapore
| | - Martin T W Chio
- Duke-NUS Graduate Medical School, Singapore
- Department of Sexually Transmitted Infections Control, National Skin Centre, Singapore
| | - Sui Sin Goh
- Department of Microbiology, Singapore General Hospital, Singapore
| | - Ai Ling Tan
- Department of Microbiology, Singapore General Hospital, Singapore
- Duke-NUS Graduate Medical School, Singapore
| | - Tse Hsien Koh
- Department of Microbiology, Singapore General Hospital, Singapore
- Duke-NUS Graduate Medical School, Singapore
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12
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Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward. Microbiol Mol Biol Rev 2019; 83:83/2/e00062-18. [PMID: 30918049 DOI: 10.1128/mmbr.00062-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Mycobacterium tuberculosis genome is more heterogenous and less genetically stable within the host than previously thought. Currently, only limited data exist on the within-host microevolution, diversity, and genetic stability of M. tuberculosis As a direct consequence, our ability to infer M. tuberculosis transmission chains and to understand the full complexity of drug resistance profiles in individual patients is limited. Furthermore, apart from the acquisition of certain drug resistance-conferring mutations, our knowledge on the function of genetic variants that emerge within a host and their phenotypic impact remains scarce. We performed a systematic literature review of whole-genome sequencing studies of serial and parallel isolates to summarize the knowledge on genetic diversity and within-host microevolution of M. tuberculosis We identified genomic loci of within-host emerged variants found across multiple studies and determined their functional relevance. We discuss important remaining knowledge gaps and finally make suggestions on the way forward.
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Daniel J, Abraham L, Martin A, Pablo X, Reyes S. Rv2477c is an antibiotic-sensitive manganese-dependent ABC-F ATPase in Mycobacterium tuberculosis. Biochem Biophys Res Commun 2018; 495:35-40. [DOI: 10.1016/j.bbrc.2017.10.168] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 10/30/2017] [Indexed: 10/18/2022]
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