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Carter JJ, Walker TM, Walker AS, Whitfield MG, Morlock GP, Lynch CI, Adlard D, Peto TEA, Posey JE, Crook DW, Fowler PW. Prediction of pyrazinamide resistance in Mycobacterium tuberculosis using structure-based machine-learning approaches. JAC Antimicrob Resist 2024; 6:dlae037. [PMID: 38500518 PMCID: PMC10946228 DOI: 10.1093/jacamr/dlae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Background Pyrazinamide is one of four first-line antibiotics used to treat tuberculosis; however, antibiotic susceptibility testing for pyrazinamide is challenging. Resistance to pyrazinamide is primarily driven by genetic variation in pncA, encoding an enzyme that converts pyrazinamide into its active form. Methods We curated a dataset of 664 non-redundant, missense amino acid mutations in PncA with associated high-confidence phenotypes from published studies and then trained three different machine-learning models to predict pyrazinamide resistance. All models had access to a range of protein structural-, chemical- and sequence-based features. Results The best model, a gradient-boosted decision tree, achieved a sensitivity of 80.2% and a specificity of 76.9% on the hold-out test dataset. The clinical performance of the models was then estimated by predicting the binary pyrazinamide resistance phenotype of 4027 samples harbouring 367 unique missense mutations in pncA derived from 24 231 clinical isolates. Conclusions This work demonstrates how machine learning can enhance the sensitivity/specificity of pyrazinamide resistance prediction in genetics-based clinical microbiology workflows, highlights novel mutations for future biochemical investigation, and is a proof of concept for using this approach in other drugs.
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Affiliation(s)
- Joshua J Carter
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Timothy M Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Michael G Whitfield
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, SAMRC Centre for Tuberculosis Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Tygerberg, South Africa
| | - Glenn P Morlock
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Charlotte I Lynch
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Dylan Adlard
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Timothy E A Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - James E Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance, University of Oxford, Oxford, UK
| | - Philip W Fowler
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
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Pang AH, Green KD, Chandrika NT, Garzan A, Punetha A, Holbrook SYL, Willby MJ, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Discovery of substituted benzyloxy-benzylamine inhibitors of acetyltransferase Eis and their anti-mycobacterial activity. Eur J Med Chem 2022; 242:114698. [PMID: 36037791 PMCID: PMC9481687 DOI: 10.1016/j.ejmech.2022.114698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/30/2022]
Abstract
A clinically significant mechanism of tuberculosis resistance to the aminoglycoside kanamycin (KAN) is its acetylation catalyzed by upregulated Mycobacterium tuberculosis (Mtb) acetyltransferase Eis. In search for inhibitors of Eis, we discovered an inhibitor with a substituted benzyloxy-benzylamine scaffold. A structure-activity relationship study of 38 compounds in this structural family yielded highly potent (IC50 ∼ 1 μM) Eis inhibitors, which did not inhibit other acetyltransferases. Crystal structures of Eis in complexes with three of the inhibitors showed that the inhibitors were bound in the aminoglycoside binding site of Eis, consistent with the competitive mode of inhibition, as established by kinetics measurements. When tested in Mtb cultures, two inhibitors (47 and 55) completely abolished resistance to KAN of the highly KAN-resistant strain Mtb mc2 6230 K204, likely due to Eis inhibition as a major mechanism. Thirteen of the compounds were toxic even in the absence of KAN to Mtb and other mycobacteria, but not to non-mycobacteria or to mammalian cells. This, yet unidentified mechanism of toxicity, distinct from Eis inhibition, will merit future studies along with further development of these molecules as anti-mycobacterial agents.
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Affiliation(s)
- Allan H Pang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Atefeh Garzan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Ankita Punetha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Selina Y L Holbrook
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA
| | - Melisa J Willby
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - James E Posey
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY, 40536-0596, USA.
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3
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Raz KM, Talarico S, Althomsons SP, Kammerer JS, Cowan LS, Haddad MB, McDaniel CJ, Wortham JM, France AM, Powell KM, Posey JE, Silk BJ. Molecular surveillance for large outbreaks of tuberculosis in the United States, 2014-2018. Tuberculosis (Edinb) 2022; 136:102232. [PMID: 35969928 PMCID: PMC9530005 DOI: 10.1016/j.tube.2022.102232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/29/2022] [Accepted: 07/13/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVE This study describes characteristics of large tuberculosis (TB) outbreaks in the United States detected using novel molecular surveillance methods during 2014-2016 and followed for 2 years through 2018. METHODS We developed 4 genotype-based detection algorithms to identify large TB outbreaks of ≥10 cases related by recent transmission during a 3-year period. We used whole-genome sequencing and epidemiologic data to assess evidence of recent transmission among cases. RESULTS There were 24 large outbreaks involving 518 cases; patients were primarily U.S.-born (85.1%) racial/ethnic minorities (84.1%). Compared with all other TB patients, patients associated with large outbreaks were more likely to report substance use, homelessness, and having been diagnosed while incarcerated. Most large outbreaks primarily occurred within residences among families and nonfamilial social contacts. A source case with a prolonged infectious period and difficulties in eliciting contacts were commonly reported contributors to transmission. CONCLUSION Large outbreak surveillance can inform targeted interventions to decrease outbreak-associated TB morbidity.
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Affiliation(s)
- Kala M Raz
- Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Sarah Talarico
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Lauren S Cowan
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Maryam B Haddad
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | | | - Krista M Powell
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - James E Posey
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Benjamin J Silk
- Centers for Disease Control and Prevention, Atlanta, GA, USA
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Georghiou SB, Rodwell TC, Korobitsyn A, Abbadi SH, Ajbani K, Alffenaar JW, Alland D, Alvarez N, Andres S, Ardizzoni E, Aubry A, Baldan R, Ballif M, Barilar I, Böttger EC, Chakravorty S, Claxton PM, Cirillo DM, Comas I, Coulter C, Denkinger CM, Derendinger B, Desmond EP, de Steenwinkel JE, Dheda K, Diacon AH, Dolinger DL, Dooley KE, Egger M, Ehsani S, Farhat MR, Fattorini L, Finci I, Le Ray LF, Furió V, Groenheit R, Gumbo T, Heysell SK, Hillemann D, Hoffmann H, Hsueh PR, Hu Y, Huang H, Hussain A, Ismail F, Izumi K, Jagielski T, Johnson JL, Kambli P, Kaniga K, Eranga Karunaratne G, Sharma MK, Keller PM, Kelly EC, Kholina M, Kohli M, Kranzer K, Laurenson IF, Limberis J, Grace Lin SY, Liu Y, López-Gavín A, Lyander A, Machado D, Martinez E, Masood F, Mitarai S, Mvelase NR, Niemann S, Nikolayevskyy V, Maurer FP, Merker M, Miotto P, Omar SV, Otto-Knapp R, Palaci M, Palacios Gutiérrez JJ, Peacock SJ, Peloquin CA, Perera J, Pierre-Audigier C, Pholwat S, Posey JE, Prammananan T, Rigouts L, Robledo J, Rockwood N, Rodrigues C, Salfinger M, Schechter MC, Seifert M, Sengstake S, Shinnick T, Shubladze N, Sintchenko V, Sirgel F, Somasundaram S, Sterling TR, Spitaleri A, Streicher E, Supply P, Svensson E, Tagliani E, Tahseen S, Takaki A, Theron G, Torrea G, Van Deun A, van Ingen J, Van Rie A, van Soolingen D, Vargas Jr R, Venter A, Veziris N, Villellas C, Viveiros M, Warren R, Wen S, Werngren J, Wilkinson RJ, Yang C, Yılmaz FF, Zhang T, Zimenkov D, Ismail N, Köser CU, Schön T. Updating the approaches to define susceptibility and resistance to anti-tuberculosis agents: implications for diagnosis and treatment. Eur Respir J 2022; 59:2200166. [PMID: 35422426 PMCID: PMC9059840 DOI: 10.1183/13993003.00166-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/05/2022] [Indexed: 11/07/2022]
Abstract
Approximately 85 000 deaths globally in 2019 were due to drug-resistant tuberculosis (TB), which corresponds to 7% of global deaths attributable to bacterial antimicrobial resistance [1]. Yet concerns have been mounting that drug-resistant TB was being underestimated because the approaches to define susceptibility and resistance to anti-TB agents had not kept up with those used for other major bacterial pathogens [2–9]. Here, we outline the recent, evidence-based initiatives spearheaded by the World Health Organization (WHO) and others to update breakpoints (traditionally referred to as critical concentrations (CCs)) that are used for phenotypic antimicrobial susceptibility testing (AST), also called drug susceptibility testing in the TB literature. Inappropriately high breakpoints have resulted in systematic false-susceptible AST results to anti-TB drugs. MIC, PK/PD and clinical outcome data should be combined when setting breakpoints to minimise the emergence and spread of antimicrobial resistance. https://bit.ly/3i43wb6
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Punetha A, Green KD, Garzan A, Thamban Chandrika N, Willby MJ, Pang AH, Hou C, Holbrook SYL, Krieger K, Posey JE, Parish T, Tsodikov OV, Garneau-Tsodikova S. Structure-based design of haloperidol analogues as inhibitors of acetyltransferase Eis from Mycobacterium tuberculosis to overcome kanamycin resistance. RSC Med Chem 2021; 12:1894-1909. [PMID: 34825186 DOI: 10.1039/d1md00239b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/13/2021] [Indexed: 12/21/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is a deadly bacterial disease. Drug-resistant strains of Mtb make eradication of TB a daunting task. Overexpression of the enhanced intracellular survival (Eis) protein by Mtb confers resistance to the second-line antibiotic kanamycin (KAN). Eis is an acetyltransferase that acetylates KAN, inactivating its antimicrobial function. Development of Eis inhibitors as KAN adjuvant therapeutics is an attractive path to forestall and overcome KAN resistance. We discovered that an antipsychotic drug, haloperidol (HPD, 1), was a potent Eis inhibitor with IC50 = 0.39 ± 0.08 μM. We determined the crystal structure of the Eis-haloperidol (1) complex, which guided synthesis of 34 analogues. The structure-activity relationship study showed that in addition to haloperidol (1), eight analogues, some of which were smaller than 1, potently inhibited Eis (IC50 ≤ 1 μM). Crystal structures of Eis in complexes with three potent analogues and droperidol (DPD), an antiemetic and antipsychotic, were determined. Three compounds partially restored KAN sensitivity of a KAN-resistant Mtb strain K204 overexpressing Eis. The Eis inhibitors generally did not exhibit cytotoxicity against mammalian cells. All tested compounds were modestly metabolically stable in human liver microsomes, exhibiting 30-60% metabolism over the course of the assay. While direct repurposing of haloperidol as an anti-TB agent is unlikely due to its neurotoxicity, this study reveals potential approaches to modifying this chemical scaffold to minimize toxicity and improve metabolic stability, while preserving potent Eis inhibition.
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Affiliation(s)
- Ankita Punetha
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Atefeh Garzan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Melisa J Willby
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention Atlanta GA 30329 USA
| | - Allan H Pang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Caixia Hou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Selina Y L Holbrook
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Kyle Krieger
- Center for Global Infectious Disease Research, Seattle Children's Research Institute 307 Westlake Avenue N Seattle WA 98109 USA
| | - James E Posey
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention Atlanta GA 30329 USA
| | - Tanya Parish
- Center for Global Infectious Disease Research, Seattle Children's Research Institute 307 Westlake Avenue N Seattle WA 98109 USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky 789 South Limestone Street Lexington KY 40536 USA
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6
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Click ES, Kurbatova EV, Alexander H, Dalton TL, Chen MP, Posey JE, Ershova J, Cegielski JP. Isoniazid and Rifampin-Resistance Mutations Associated With Resistance to Second-Line Drugs and With Sputum Culture Conversion. J Infect Dis 2021; 221:2072-2082. [PMID: 32002554 DOI: 10.1093/infdis/jiaa042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/28/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Mutations in the genes inhA, katG, and rpoB confer resistance to anti-tuberculosis (TB) drugs isoniazid and rifampin. We questioned whether specific mutations in these genes were associated with different clinical and microbiological characteristics. METHODS In a multicountry prospective cohort study of multidrug-resistant TB, we identified inhA, katG, and rpoB mutations in sputum isolates using the Hain MTBDRplus line probe assay. For specific mutations, we performed bivariate analysis to determine relative risk of baseline or acquired resistance to other TB drugs. We compared time to sputum culture conversion (TSCC) using Kaplan-Meier curves and stratified Cox regression. RESULTS In total, 447 participants enrolled from January 2005 to December 2008 from 7 countries were included. Relative to rpoB S531L, isolates with rpoB D516V had less cross-resistance to rifabutin, increased baseline resistance to other drugs, and increased acquired fluoroquinolone resistance. Relative to mutation of katG only, mutation of inhA promoter and katG was associated with baseline extensively drug resistant (XDR) TB, increased acquired fluoroquinolone resistance, and slower TSCC (125.5 vs 89.0 days). CONCLUSIONS Specific mutations in inhA and katG are associated with differences in resistance to other drugs and TSCC. Molecular testing may make it possible to tailor treatment and assess additional drug resistance risk according to specific mutation profile.
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Affiliation(s)
- Eleanor S Click
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ekaterina V Kurbatova
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Heather Alexander
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tracy L Dalton
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael P Chen
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - James E Posey
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Julia Ershova
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J Peter Cegielski
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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7
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Punetha A, Ngo HX, Holbrook SYL, Green KD, Willby MJ, Bonnett SA, Krieger K, Dennis EK, Posey JE, Parish T, Tsodikov OV, Garneau-Tsodikova S. Structure-Guided Optimization of Inhibitors of Acetyltransferase Eis from Mycobacterium tuberculosis. ACS Chem Biol 2020; 15:1581-1594. [PMID: 32421305 DOI: 10.1021/acschembio.0c00184] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enhanced intracellular survival (Eis) protein of Mycobacterium tuberculosis (Mtb) is a versatile acetyltransferase that multiacetylates aminoglycoside antibiotics abolishing their binding to the bacterial ribosome. When overexpressed as a result of promoter mutations, Eis causes drug resistance. In an attempt to overcome the Eis-mediated kanamycin resistance of Mtb, we designed and optimized structurally unique thieno[2,3-d]pyrimidine Eis inhibitors toward effective kanamycin adjuvant combination therapy. We obtained 12 crystal structures of enzyme-inhibitor complexes, which guided our rational structure-based design of 72 thieno[2,3-d]pyrimidine analogues divided into three families. We evaluated the potency of these inhibitors in vitro as well as their ability to restore the activity of kanamycin in a resistant strain of Mtb, in which Eis was upregulated. Furthermore, we evaluated the metabolic stability of 11 compounds in vitro. This study showcases how structural information can guide Eis inhibitor design.
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Affiliation(s)
- Ankita Punetha
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Huy X. Ngo
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Selina Y. L. Holbrook
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Keith D. Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Melisa J. Willby
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Shilah A. Bonnett
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102, United States
| | - Kyle Krieger
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102, United States
- Center for Global Infectious Disease, Seattle Children’s Research Institute, Seattle Children’s Hospital, Seattle, Washington 98145, United States
| | - Emily K. Dennis
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - James E. Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington 98102, United States
- Center for Global Infectious Disease, Seattle Children’s Research Institute, Seattle Children’s Hospital, Seattle, Washington 98145, United States
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
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Abstract
Rapid advances in DNA sequencing technology ("next-generation sequencing") have inspired optimism about the potential of human genomics for "precision medicine." Meanwhile, pathogen genomics is already delivering "precision public health" through more effective investigations of outbreaks of foodborne illnesses, better-targeted tuberculosis control, and more timely and granular influenza surveillance to inform the selection of vaccine strains. In this article, we describe how public health agencies have been adopting pathogen genomics to improve their effectiveness in almost all domains of infectious disease. This momentum is likely to continue, given the ongoing development in sequencing and sequencing-related technologies.
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Affiliation(s)
- Gregory L Armstrong
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - Duncan R MacCannell
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - Jill Taylor
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - Heather A Carleton
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - Elizabeth B Neuhaus
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - Richard S Bradbury
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - James E Posey
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
| | - Marta Gwinn
- From the National Center for Emerging and Zoonotic Infectious Diseases (G.L.A., D.R.M., H.A.C.), the National Center for Immunization and Respiratory Diseases (E.B.N.), the Center for Global Health (R.S.B.), and the National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (J.E.P.), Centers for Disease Control and Prevention, and CFOL International (M.G.) - all in Atlanta; and the Wadsworth Center, New York State Department of Health, Albany (J.T.)
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Althomsons SP, Hill AN, Harrist AV, France AM, Powell KM, Posey JE, Cowan LS, Navin TR. Statistical Method to Detect Tuberculosis Outbreaks among Endemic Clusters in a Low-Incidence Setting. Emerg Infect Dis 2019; 24:573-575. [PMID: 29460749 PMCID: PMC5823347 DOI: 10.3201/eid2403.171613] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We previously reported use of genotype surveillance data to predict outbreaks among incident tuberculosis clusters. We propose a method to detect possible outbreaks among endemic tuberculosis clusters. We detected 15 possible outbreaks, of which 10 had epidemiologic data or whole-genome sequencing results. Eight outbreaks were corroborated.
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10
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Desilva M, Moore N, Thai D, Grimm MB, Sabuwala N, Brueshaber M, Gordon S, Andersen L, Hall V, Buuck S, Hickman C, Stinebaugh K, Silk B, Raz K, Talarico S, Wortham J, Kingdon E, Pistulka G, Guerard K, Cowan L, Posey JE, Snippes Vagnone PM, McCullough J, Tsukayama D, Mody RK, Ehresmann K. 769. An Outbreak of Multidrug-Resistant Tuberculosis, Minnesota 2016–2017. Open Forum Infect Dis 2018. [PMCID: PMC6254059 DOI: 10.1093/ofid/ofy210.776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Methods Results Conclusion Disclosures
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Affiliation(s)
- Malini Desilva
- Infectious Disease Epidemiology, Prevention and Control Division, Minnesota Department of Health, Saint Paul, Minnesota
| | - Nora Moore
- Saint Paul – Ramsey County Public Health, Saint Paul, Minnesota
| | - Dzung Thai
- Infectious Disease Epidemiology, Prevention and Control Division, Minnesota Department of Health, Saint Paul, Minnesota
| | - Mary Beth Grimm
- Saint Paul – Ramsey County Public Health, Saint Paul, Minnesota
| | - Nadya Sabuwala
- Infectious Disease Epidemiology, Prevention and Control Division, Minnesota Department of Health, Saint Paul, Minnesota
| | - Milayna Brueshaber
- Infectious Disease Epidemiology, Prevention and Control Division, Minnesota Department of Health, Saint Paul, Minnesota
| | - Sarah Gordon
- Infectious Disease Epidemiology, Prevention and Control Division, Minnesota Department of Health, Saint Paul, Minnesota
| | - Laura Andersen
- Saint Paul – Ramsey County Public Health, Saint Paul, Minnesota
| | - Victoria Hall
- Infectious Disease Epidemiology, Prevention and Control Division, Minnesota Department of Health, Saint Paul, Minnesota,Epidemic Intelligence Service Program, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sean Buuck
- Infectious Disease Epidemiology, Prevention and Control Division, Minnesota Department of Health, Saint Paul, Minnesota
| | - Cynthia Hickman
- Infectious Disease Epidemiology, Prevention and Control Division, Minnesota Department of Health, Saint Paul, Minnesota
| | - Katie Stinebaugh
- Infectious Disease Epidemiology, Prevention and Control Division, Minnesota Department of Health, Saint Paul, Minnesota
| | - Benjamin Silk
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Kayla Raz
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sarah Talarico
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jonathan Wortham
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Elisabeth Kingdon
- Infectious Disease Epidemiology, Prevention and Control Division, Minnesota Department of Health, Saint Paul, Minnesota
| | - Gina Pistulka
- Saint Paul – Ramsey County Public Health, Saint Paul, Minnesota
| | - Krissie Guerard
- Infectious Disease Epidemiology, Prevention and Control Division, Minnesota Department of Health, Saint Paul, Minnesota
| | - Lauren Cowan
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - James E Posey
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Joel McCullough
- Saint Paul – Ramsey County Public Health, Saint Paul, Minnesota
| | | | - Rajal K Mody
- Division of State and Local Readiness, Office of Public Health Preparedness and Response, CDC, Atlanta, Georgia
| | - Kristen Ehresmann
- Infectious Disease Epidemiology, Prevention and Control Division, Minnesota Department of Health, Saint Paul, Minnesota
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11
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Allix-Béguec C, Arandjelovic I, Bi L, Beckert P, Bonnet M, Bradley P, Cabibbe AM, Cancino-Muñoz I, Caulfield MJ, Chaiprasert A, Cirillo DM, Clifton DA, Comas I, Crook DW, De Filippo MR, de Neeling H, Diel R, Drobniewski FA, Faksri K, Farhat MR, Fleming J, Fowler P, Fowler TA, Gao Q, Gardy J, Gascoyne-Binzi D, Gibertoni-Cruz AL, Gil-Brusola A, Golubchik T, Gonzalo X, Grandjean L, He G, Guthrie JL, Hoosdally S, Hunt M, Iqbal Z, Ismail N, Johnston J, Khanzada FM, Khor CC, Kohl TA, Kong C, Lipworth S, Liu Q, Maphalala G, Martinez E, Mathys V, Merker M, Miotto P, Mistry N, Moore DAJ, Murray M, Niemann S, Omar SV, Ong RTH, Peto TEA, Posey JE, Prammananan T, Pym A, Rodrigues C, Rodrigues M, Rodwell T, Rossolini GM, Sánchez Padilla E, Schito M, Shen X, Shendure J, Sintchenko V, Sloutsky A, Smith EG, Snyder M, Soetaert K, Starks AM, Supply P, Suriyapol P, Tahseen S, Tang P, Teo YY, Thuong TNT, Thwaites G, Tortoli E, van Soolingen D, Walker AS, Walker TM, Wilcox M, Wilson DJ, Wyllie D, Yang Y, Zhang H, Zhao Y, Zhu B. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing. N Engl J Med 2018; 379:1403-1415. [PMID: 30280646 PMCID: PMC6121966 DOI: 10.1056/nejmoa1800474] [Citation(s) in RCA: 300] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND The World Health Organization recommends drug-susceptibility testing of Mycobacterium tuberculosis complex for all patients with tuberculosis to guide treatment decisions and improve outcomes. Whether DNA sequencing can be used to accurately predict profiles of susceptibility to first-line antituberculosis drugs has not been clear. METHODS We obtained whole-genome sequences and associated phenotypes of resistance or susceptibility to the first-line antituberculosis drugs isoniazid, rifampin, ethambutol, and pyrazinamide for isolates from 16 countries across six continents. For each isolate, mutations associated with drug resistance and drug susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These profiles were predicted to be susceptible to all four drugs (i.e., pansusceptible) if they were predicted to be susceptible to isoniazid and to the other drugs or if they contained mutations of unknown association in genes that affect susceptibility to the other drugs. We simulated the way in which the negative predictive value changed with the prevalence of drug resistance. RESULTS A total of 10,209 isolates were analyzed. The largest proportion of phenotypes was predicted for rifampin (9660 [95.4%] of 10,130) and the smallest was predicted for ethambutol (8794 [89.8%] of 9794). Resistance to isoniazid, rifampin, ethambutol, and pyrazinamide was correctly predicted with 97.1%, 97.5%, 94.6%, and 91.3% sensitivity, respectively, and susceptibility to these drugs was correctly predicted with 99.0%, 98.8%, 93.6%, and 96.8% specificity. Of the 7516 isolates with complete phenotypic drug-susceptibility profiles, 5865 (78.0%) had complete genotypic predictions, among which 5250 profiles (89.5%) were correctly predicted. Among the 4037 phenotypic profiles that were predicted to be pansusceptible, 3952 (97.9%) were correctly predicted. CONCLUSIONS Genotypic predictions of the susceptibility of M. tuberculosis to first-line drugs were found to be correlated with phenotypic susceptibility to these drugs. (Funded by the Bill and Melinda Gates Foundation and others.).
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12
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Ngo HX, Green KD, Gajadeera CS, Willby MJ, Holbrook SYL, Hou C, Garzan A, Mayhoub AS, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Potent 1,2,4-Triazino[5,6 b]indole-3-thioether Inhibitors of the Kanamycin Resistance Enzyme Eis from Mycobacterium tuberculosis. ACS Infect Dis 2018; 4:1030-1040. [PMID: 29601176 DOI: 10.1021/acsinfecdis.8b00074] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A common cause of resistance to kanamycin (KAN) in tuberculosis is overexpression of the enhanced intracellular survival (Eis) protein. Eis is an acetyltransferase that multiacetylates KAN and other aminoglycosides, rendering them unable to bind the bacterial ribosome. By high-throughput screening, a series of substituted 1,2,4-triazino[5,6 b]indole-3-thioether molecules were identified as effective Eis inhibitors. Herein, we purchased 17 and synthesized 22 new compounds, evaluated their potency, and characterized their steady-state kinetics. Four inhibitors were found not only to inhibit Eis in vitro, but also to act as adjuvants of KAN and partially restore KAN sensitivity in a Mycobacterium tuberculosis KAN-resistant strain in which Eis is upregulated. A crystal structure of Eis in complex with a potent inhibitor and CoA shows that the inhibitors bind in the aminoglycoside binding site snugly inserted into a hydrophobic cavity. These inhibitors will undergo preclinical development as novel KAN adjuvant therapies to treat KAN-resistant tuberculosis.
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Affiliation(s)
- Huy X. Ngo
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Keith D. Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Chathurada S. Gajadeera
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Melisa J. Willby
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329, United States
| | - Selina Y. L. Holbrook
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Atefeh Garzan
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Abdelrahman S. Mayhoub
- Department of Medicinal Chemistry and Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
| | - James E. Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Georgia 30329, United States
| | - Oleg. V. Tsodikov
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, University of Kentucky, Lee T. Todd, Jr. Building, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Department of Medicinal Chemistry and Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109, United States
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13
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Green KD, Biswas T, Pang AH, Willby MJ, Reed MS, Stuchlik O, Pohl J, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Acetylation by Eis and Deacetylation by Rv1151c of Mycobacterium tuberculosis HupB: Biochemical and Structural Insight. Biochemistry 2018; 57:781-790. [PMID: 29345920 DOI: 10.1021/acs.biochem.7b01089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial nucleoid-associated proteins (NAPs) are critical to genome integrity and chromosome maintenance. Post-translational modifications of bacterial NAPs appear to function similarly to their better studied mammalian counterparts. The histone-like NAP HupB from Mycobacterium tuberculosis (Mtb) was previously observed to be acetylated by the acetyltransferase Eis, leading to genome reorganization. We report biochemical and structural aspects of acetylation of HupB by Eis. We also found that the SirT-family NAD+-dependent deacetylase Rv1151c from Mtb deacetylated HupB in vitro and characterized the deacetylation kinetics. We propose that activities of Eis and Rv1151c could regulate the acetylation status of HupB to remodel the mycobacterial chromosome in response to environmental changes.
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Affiliation(s)
- Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Tapan Biswas
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Allan H Pang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | | | | | | | | | | | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536-0596, United States
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14
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Garzan A, Willby MJ, Ngo HX, Gajadeera CS, Green KD, Holbrook SYL, Hou C, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Combating Enhanced Intracellular Survival (Eis)-Mediated Kanamycin Resistance of Mycobacterium tuberculosis by Novel Pyrrolo[1,5-a]pyrazine-Based Eis Inhibitors. ACS Infect Dis 2017; 3:302-309. [PMID: 28192916 DOI: 10.1021/acsinfecdis.6b00193] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Tuberculosis (TB) remains one of the leading causes of mortality worldwide. Hence, the identification of highly effective antitubercular drugs with novel modes of action is crucial. In this paper, we report the discovery and development of pyrrolo[1,5-a]pyrazine-based analogues as highly potent inhibitors of the Mycobacterium tuberculosis (Mtb) acetyltransferase enhanced intracellular survival (Eis), whose up-regulation causes clinically observed resistance to the aminoglycoside (AG) antibiotic kanamycin A (KAN). We performed a structure-activity relationship (SAR) study to optimize these compounds as potent Eis inhibitors both against purified enzyme and in mycobacterial cells. A crystal structure of Eis in complex with one of the most potent inhibitors reveals that the compound is bound to Eis in the AG binding pocket, serving as the structural basis for the SAR. These Eis inhibitors have no observed cytotoxicity to mammalian cells and are promising leads for the development of innovative AG adjuvant therapies against drug-resistant TB.
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Affiliation(s)
- Atefeh Garzan
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Melisa J. Willby
- Laboratory Branch, Division of Tuberculosis
Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and
TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, United States
| | - Huy X. Ngo
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Chathurada S. Gajadeera
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Keith D. Green
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Selina Y. L. Holbrook
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - James E. Posey
- Laboratory Branch, Division of Tuberculosis
Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and
TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, United States
| | - Oleg V. Tsodikov
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical
Sciences, College of Pharmacy, University of Kentucky, 789 South
Limestone Street, Lexington, Kentucky 40536-0596, United States
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15
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Garzan A, Willby MJ, Ngo HX, Gajadeera CS, Green KD, Holbrook SYL, Hou C, Posey JE, Tsodikov OV, Garneau-Tsodikova S. Combating Enhanced Intracellular Survival (Eis)-Mediated Kanamycin Resistance of Mycobacterium tuberculosis by Novel Pyrrolo[1,5-a]pyrazine-Based Eis Inhibitors. ACS Infect Dis 2017. [PMID: 28192916 DOI: 10.1021/acsinfecdis.6b00193.] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) remains one of the leading causes of mortality worldwide. Hence, the identification of highly effective antitubercular drugs with novel modes of action is crucial. In this paper, we report the discovery and development of pyrrolo[1,5-a]pyrazine-based analogues as highly potent inhibitors of the Mycobacterium tuberculosis (Mtb) acetyltransferase enhanced intracellular survival (Eis), whose up-regulation causes clinically observed resistance to the aminoglycoside (AG) antibiotic kanamycin A (KAN). We performed a structure-activity relationship (SAR) study to optimize these compounds as potent Eis inhibitors both against purified enzyme and in mycobacterial cells. A crystal structure of Eis in complex with one of the most potent inhibitors reveals that the compound is bound to Eis in the AG binding pocket, serving as the structural basis for the SAR. These Eis inhibitors have no observed cytotoxicity to mammalian cells and are promising leads for the development of innovative AG adjuvant therapies against drug-resistant TB.
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Affiliation(s)
- Atefeh Garzan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Melisa J Willby
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, Georgia 30329, United States
| | - Huy X Ngo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Chathurada S Gajadeera
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Keith D Green
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Selina Y L Holbrook
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - James E Posey
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, Georgia 30329, United States
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
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16
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Garzan A, Willby MJ, Green KD, Tsodikov OV, Posey JE, Garneau-Tsodikova S. Discovery and Optimization of Two Eis Inhibitor Families as Kanamycin Adjuvants against Drug-Resistant M. tuberculosis. ACS Med Chem Lett 2016; 7:1219-1221. [PMID: 27994767 DOI: 10.1021/acsmedchemlett.6b00261] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/15/2016] [Indexed: 11/29/2022] Open
Abstract
Drug-resistant tuberculosis (TB) is a global threat and innovative approaches such as using adjuvants of anti-TB therapeutics are required to combat it. High-throughput screening yielded two lead scaffolds of inhibitors of Mycobacterium tuberculosis (Mtb) acetyltransferase Eis, whose upregulation causes resistance to the anti-TB drug kanamycin (KAN). Chemical optimization on these scaffolds resulted in potent Eis inhibitors. One compound restored the activity of KAN in a KAN-resistant Mtb strain. Model structures of Eis-inhibitor complexes explain the structure-activity relationship.
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Affiliation(s)
- Atefeh Garzan
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Melisa J. Willby
- Mycobacteriology
Laboratory Branch, Division of Tuberculosis Elimination, National
Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Keith D. Green
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Oleg V. Tsodikov
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
| | - James E. Posey
- Mycobacteriology
Laboratory Branch, Division of Tuberculosis Elimination, National
Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, United States
| | - Sylvie Garneau-Tsodikova
- Department
of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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17
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Garzan A, Willby MJ, Green KD, Gajadeera CS, Hou C, Tsodikov OV, Posey JE, Garneau-Tsodikova S. Sulfonamide-Based Inhibitors of Aminoglycoside Acetyltransferase Eis Abolish Resistance to Kanamycin in Mycobacterium tuberculosis. J Med Chem 2016; 59:10619-10628. [PMID: 27933949 DOI: 10.1021/acs.jmedchem.6b01161] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A two-drug combination therapy where one drug targets an offending cell and the other targets a resistance mechanism to the first drug is a time-tested, yet underexploited approach to combat or prevent drug resistance. By high-throughput screening, we identified a sulfonamide scaffold that served as a pharmacophore to generate inhibitors of Mycobacterium tuberculosis acetyltransferase Eis, whose upregulation causes resistance to the aminoglycoside (AG) antibiotic kanamycin A (KAN) in Mycobacterium tuberculosis. Rational systematic derivatization of this scaffold to maximize Eis inhibition and abolish the Eis-mediated KAN resistance of M. tuberculosis yielded several highly potent agents. A crystal structure of Eis in complex with one of the most potent inhibitors revealed that the inhibitor bound Eis in the AG-binding pocket held by a conformationally malleable region of Eis (residues 28-37) bearing key hydrophobic residues. These Eis inhibitors are promising leads for preclinical development of innovative AG combination therapies against resistant TB.
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Affiliation(s)
- Atefeh Garzan
- University of Kentucky , Department of Pharmaceutical Sciences, College of Pharmacy, 789 South Limestone St., Lexington, Kentucky 40536-0596, United States
| | - Melisa J Willby
- Mycobacteriology Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, Georgia 30333, United States
| | - Keith D Green
- University of Kentucky , Department of Pharmaceutical Sciences, College of Pharmacy, 789 South Limestone St., Lexington, Kentucky 40536-0596, United States
| | - Chathurada S Gajadeera
- University of Kentucky , Department of Pharmaceutical Sciences, College of Pharmacy, 789 South Limestone St., Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- University of Kentucky , Department of Pharmaceutical Sciences, College of Pharmacy, 789 South Limestone St., Lexington, Kentucky 40536-0596, United States
| | - Oleg V Tsodikov
- University of Kentucky , Department of Pharmaceutical Sciences, College of Pharmacy, 789 South Limestone St., Lexington, Kentucky 40536-0596, United States
| | - James E Posey
- Mycobacteriology Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention , Atlanta, Georgia 30333, United States
| | - Sylvie Garneau-Tsodikova
- University of Kentucky , Department of Pharmaceutical Sciences, College of Pharmacy, 789 South Limestone St., Lexington, Kentucky 40536-0596, United States
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18
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Willby MJ, Green KD, Gajadeera CS, Hou C, Tsodikov OV, Posey JE, Garneau-Tsodikova S. Potent Inhibitors of Acetyltransferase Eis Overcome Kanamycin Resistance in Mycobacterium tuberculosis. ACS Chem Biol 2016; 11:1639-46. [PMID: 27010218 DOI: 10.1021/acschembio.6b00110] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A major cause of tuberculosis (TB) resistance to the aminoglycoside kanamycin (KAN) is the Mycobacterium tuberculosis (Mtb) acetyltransferase Eis. Upregulation of this enzyme is responsible for inactivation of KAN through acetylation of its amino groups. A 123 000-compound high-throughput screen (HTS) yielded several small-molecule Eis inhibitors that share an isothiazole S,S-dioxide heterocyclic core. These were investigated for their structure-activity relationships. Crystal structures of Eis in complex with two potent inhibitors show that these molecules are bound in the conformationally adaptable aminoglycoside binding site of the enzyme, thereby obstructing binding of KAN for acetylation. Importantly, we demonstrate that several Eis inhibitors, when used in combination with KAN against resistant Mtb, efficiently overcome KAN resistance. This approach paves the way toward development of novel combination therapies against aminoglycoside-resistant TB.
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Affiliation(s)
- Melisa J. Willby
- Division of Tuberculosis
Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and
TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, United States
| | - Keith D. Green
- Department
of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Chathurada S. Gajadeera
- Department
of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Caixia Hou
- Department
of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - Oleg V. Tsodikov
- Department
of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
| | - James E. Posey
- Division of Tuberculosis
Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and
TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia 30329, United States
| | - Sylvie Garneau-Tsodikova
- Department
of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536-0596, United States
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19
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Pavlicek RL, Fine-Coulson K, Gupta T, Quinn FD, Posey JE, Willby M, Castro-Garza J, Karls RK. Rv3351c, a Mycobacterium tuberculosis gene that affects bacterial growth and alveolar epithelial cell viability. Can J Microbiol 2015; 61:938-47. [PMID: 26492080 DOI: 10.1139/cjm-2015-0528] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Despite the interactions known to occur between various lower respiratory tract pathogens and alveolar epithelial cells (AECs), few reports examine factors influencing the interplay between Mycobacterium tuberculosis bacilli and AECs during infection. Importantly, in vitro studies have demonstrated that the M. tuberculosis hbha and esxA gene products HBHA and ESAT6 directly or indirectly influence AEC survival. In this report, we identify Rv3351c as another M. tuberculosis gene that impacts the fate of both the pathogen and AEC host. Intracellular replication of an Rv3351c mutant in the human AEC type II pneumocyte cell line A549 was markedly reduced relative to the complemented mutant and parent strain. Deletion of Rv3351c diminished the release of lactate dehydrogenase and decreased uptake of trypan blue vital stain by host cells infected with M. tuberculosis bacilli, suggesting attenuated cytotoxic effects. Interestingly, an isogenic hbha mutant displayed reductions in AEC killing similar to those observed for the Rv3351c mutant. This opens the possibility that multiple M. tuberculosis gene products interact with AECs. We also observed that Rv3351c aids intracellular replication and survival of M. tuberculosis in macrophages. This places Rv3351c in the same standing as HBHA and ESAT6, which are important factors in AECs and macrophages. Defining the mechanism(s) by which Rv3351c functions to aid pathogen survival within the host may lead to new drug or vaccine targets.
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Affiliation(s)
- Rebecca L Pavlicek
- a Department of Infectious Diseases, University of Georgia, 220 Riverbend Road, Athens, GA 30602, USA
| | - Kari Fine-Coulson
- a Department of Infectious Diseases, University of Georgia, 220 Riverbend Road, Athens, GA 30602, USA
| | - Tuhina Gupta
- a Department of Infectious Diseases, University of Georgia, 220 Riverbend Road, Athens, GA 30602, USA
| | - Frederick D Quinn
- a Department of Infectious Diseases, University of Georgia, 220 Riverbend Road, Athens, GA 30602, USA
| | - James E Posey
- b Mycobacteriology Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Melisa Willby
- b Mycobacteriology Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Jorge Castro-Garza
- c Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, N.L. 64720, Mexico
| | - Russell K Karls
- a Department of Infectious Diseases, University of Georgia, 220 Riverbend Road, Athens, GA 30602, USA
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20
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Willby M, Sikes RD, Malik S, Metchock B, Posey JE. Correlation between GyrA substitutions and ofloxacin, levofloxacin, and moxifloxacin cross-resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2015; 59:5427-34. [PMID: 26100699 PMCID: PMC4538465 DOI: 10.1128/aac.00662-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/15/2015] [Indexed: 11/20/2022] Open
Abstract
The newer fluoroquinolones moxifloxacin (MXF) and levofloxacin (LVX) are becoming more common components of tuberculosis (TB) treatment regimens. However, the critical concentrations for testing susceptibility of Mycobacterium tuberculosis to MXF and LVX are not yet well established. Additionally, the degree of cross-resistance between ofloxacin (OFX) and these newer fluoroquinolones has not been thoroughly investigated. In this study, the MICs for MXF and LVX and susceptibility to the critical concentration of OFX were determined using the agar proportion method for 133 isolates of M. tuberculosis. Most isolates resistant to OFX had LVX MICs of >1 μg/ml and MXF MICs of >0.5 μg/ml. The presence of mutations within the gyrA quinolone resistance-determining regions (QRDR) correlated well with increased MICs, and the level of LVX and MXF resistance was dependent on the specific gyrA mutation present. Substitutions Ala90Val, Asp94Ala, and Asp94Tyr resulted in low-level MXF resistance (MICs were >0.5 but ≤2 μg/ml), while other mutations led to MXF MICs of >2 μg/ml. Based on these results, a critical concentration of 1 μg/ml is suggested for LVX and 0.5 μg/ml for MXF drug susceptibility testing by agar proportion with reflex testing for MXF at 2 μg/ml.
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Affiliation(s)
- Melisa Willby
- Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - R David Sikes
- Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Seidu Malik
- Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Beverly Metchock
- Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - James E Posey
- Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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21
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Nandakumar S, Kannanganat S, Posey JE, Amara RR, Sable SB. Attrition of T-cell functions and simultaneous upregulation of inhibitory markers correspond with the waning of BCG-induced protection against tuberculosis in mice. PLoS One 2014; 9:e113951. [PMID: 25419982 PMCID: PMC4242676 DOI: 10.1371/journal.pone.0113951] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/01/2014] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium bovis bacille Calmette-Guérin (BCG) is the most widely used live attenuated vaccine. However, the correlates of protection and waning of its immunity against tuberculosis is poorly understood. In this study, we correlated the longitudinal changes in the magnitude and functional quality of CD4+ and CD8+ T-cell response over a period of two years after mucosal or parenteral BCG vaccination with the strength of protection against Mycobacterium tuberculosis in mice. The BCG vaccination-induced CD4+ and CD8+ T cells exhibited comparable response kinetics but distinct functional attributes in-terms of IFN-γ, IL-2 and TNF-α co-production and CD62L memory marker expression. Despite a near life-long BCG persistence and the induction of enduring CD4+ T-cell responses characterized by IFN-γ and/or TNF-α production with comparable protection, the protective efficacy waned regardless of the route of vaccination. The progressive decline in the multifactorial functional abilities of CD4+ and CD8+ T cells in-terms of type-1 cytokine production, proliferation and cytolytic potential corresponded with the waning of protection against M. tuberculosis infection. In addition, simultaneous increase in the dysfunctional and terminally-differentiated T cells expressing CTLA-4, KLRG-1 and IL-10 during the contraction phase of BCG-induced response coincided with the loss of protection. Our results question the empirical development of BCG-booster vaccines and emphasize the pursuit of strategies that maintain superior T-cell functional capacity. Furthermore, our results underscore the importance of understanding the comprehensive functional dynamics of antigen-specific T-cell responses in addition to cytokine polyfunctionality in BCG-vaccinated hosts while optimizing novel vaccination strategies against tuberculosis.
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Affiliation(s)
- Subhadra Nandakumar
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sunil Kannanganat
- Department of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - James E. Posey
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rama Rao Amara
- Department of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Suraj B. Sable
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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22
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Gajadeera C, Willby MJ, Green KD, Shaul P, Fridman M, Garneau-Tsodikova S, Posey JE, Tsodikov OV. Antimycobacterial activity of DNA intercalator inhibitors of Mycobacterium tuberculosis primase DnaG. J Antibiot (Tokyo) 2014; 68:153-7. [PMID: 25248725 DOI: 10.1038/ja.2014.131] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/29/2014] [Accepted: 08/13/2014] [Indexed: 11/09/2022]
Abstract
Owing to the rise in drug resistance in tuberculosis combined with the global spread of its causative pathogen, Mycobacterium tuberculosis (Mtb), innovative anti mycobacterial agents are urgently needed. Recently, we developed a novel primase-pyrophosphatase assay and used it to discover inhibitors of an essential Mtb enzyme, primase DnaG (Mtb DnaG), a promising and unexplored potential target for novel antituberculosis chemotherapeutics. Doxorubicin, an anthracycline antibiotic used as an anticancer drug, was found to be a potent inhibitor of Mtb DnaG. In this study, we investigated both inhibition of Mtb DnaG and the inhibitory activity against in vitro growth of Mtb and M. smegmatis (Msm) by other anthracyclines, daunorubicin and idarubicin, as well as by less cytotoxic DNA intercalators: aloe-emodin, rhein and a mitoxantrone derivative. Generally, low-μM inhibition of Mtb DnaG by the anthracyclines was correlated with their low-μM minimum inhibitory concentrations. Aloe-emodin displayed threefold weaker potency than doxorubicin against Mtb DnaG and similar inhibition of Msm (but not Mtb) in the mid-μM range, whereas rhein (a close analog of aloe-emodin) and a di-glucosylated mitoxantrone derivative did not show significant inhibition of Mtb DnaG or antimycobacterial activity. Taken together, these observations strongly suggest that several clinically used anthracyclines and aloe-emodin target mycobacterial primase, setting the stage for a more extensive exploration of this enzyme as an antibacterial target.
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Affiliation(s)
- Chathurada Gajadeera
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Melisa J Willby
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Keith D Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
| | - Pazit Shaul
- School of Chemistry, Tel Aviv University, Tel Aviv, Israel
| | - Micha Fridman
- School of Chemistry, Tel Aviv University, Tel Aviv, Israel
| | | | - James E Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA
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23
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Nandakumar S, Kannanganat S, Dobos KM, Lucas M, Spencer JS, Fang S, McDonald MA, Pohl J, Birkness K, Chamcha V, Ramirez MV, Plikaytis BB, Posey JE, Amara RR, Sable SB. O-mannosylation of the Mycobacterium tuberculosis adhesin Apa is crucial for T cell antigenicity during infection but is expendable for protection. PLoS Pathog 2013; 9:e1003705. [PMID: 24130497 PMCID: PMC3795050 DOI: 10.1371/journal.ppat.1003705] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 08/28/2013] [Indexed: 01/24/2023] Open
Abstract
Glycosylation is the most abundant post-translational polypeptide chain modification in nature. Although carbohydrate modification of protein antigens from many microbial pathogens constitutes important components of B cell epitopes, the role in T cell immunity is not completely understood. Here, using ELISPOT and polychromatic flow cytometry, we show that O-mannosylation of the adhesin, Apa, of Mycobacterium tuberculosis (Mtb) is crucial for its T cell antigenicity in humans and mice after infection. However, subunit vaccination with both mannosylated and non-mannosylated Apa induced a comparable magnitude and quality of T cell response and imparted similar levels of protection against Mtb challenge in mice. Both forms equally improved waning BCG vaccine-induced protection in elderly mice after subunit boosting. Thus, O-mannosylation of Apa is required for antigenicity but appears to be dispensable for its immunogenicity and protective efficacy in mice. These results have implications for the development of subunit vaccines using post-translationally modified proteins such as glycoproteins against infectious diseases like tuberculosis.
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Affiliation(s)
- Subhadra Nandakumar
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sunil Kannanganat
- Department of Microbiology and Immunology, Yerkes National Primate Research Center and Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Karen M. Dobos
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Megan Lucas
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - John S. Spencer
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Sunan Fang
- Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Melissa A. McDonald
- Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jan Pohl
- Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Kristin Birkness
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Venkateswarlu Chamcha
- Department of Microbiology and Immunology, Yerkes National Primate Research Center and Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Melissa V. Ramirez
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bonnie B. Plikaytis
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - James E. Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rama Rao Amara
- Department of Microbiology and Immunology, Yerkes National Primate Research Center and Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Suraj B. Sable
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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24
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Kalokhe AS, Shafiq M, Lee JC, Metchock B, Posey JE, Ray SM, Anderson A, Wang YF, Nguyen MLT. Discordance in Mycobacterium tuberculosis rifampin susceptibility. Emerg Infect Dis 2012; 18:537-9. [PMID: 22377132 PMCID: PMC3309586 DOI: 10.3201/eid1803.111357] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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25
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Malik S, Willby M, Sikes D, Tsodikov OV, Posey JE. New insights into fluoroquinolone resistance in Mycobacterium tuberculosis: functional genetic analysis of gyrA and gyrB mutations. PLoS One 2012; 7:e39754. [PMID: 22761889 PMCID: PMC3386181 DOI: 10.1371/journal.pone.0039754] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 05/30/2012] [Indexed: 11/20/2022] Open
Abstract
Fluoroquinolone antibiotics are among the most potent second-line drugs used for treatment of multidrug-resistant tuberculosis (MDR TB), and resistance to this class of antibiotics is one criterion for defining extensively drug resistant tuberculosis (XDR TB). Fluoroquinolone resistance in Mycobacterium tuberculosis has been associated with modification of the quinolone resistance determining region (QRDR) of gyrA. Recent studies suggest that amino acid substitutions in gyrB may also play a crucial role in resistance, but functional genetic studies of these mutations in M. tuberculosis are lacking. In this study, we examined twenty six mutations in gyrase genes gyrA (seven) and gyrB (nineteen) to determine the clinical relevance and role of these mutations in fluoroquinolone resistance. Transductants or clinical isolates harboring T80A, T80A+A90G, A90G, G247S and A384V gyrA mutations were susceptible to all fluoroquinolones tested. The A74S mutation conferred low-level resistance to moxifloxacin but susceptibility to ciprofloxacin, levofloxacin and ofloxacin, and the A74S+D94G double mutation conferred cross resistance to all the fluoroquinolones tested. Functional genetic analysis and structural modeling of gyrB suggest that M330I, V340L, R485C, D500A, D533A, A543T, A543V and T546M mutations are not sufficient to confer resistance as determined by agar proportion. Only three mutations, N538D, E540V and R485C+T539N, conferred resistance to all four fluoroquinolones in at least one genetic background. The D500H and D500N mutations conferred resistance only to levofloxacin and ofloxacin while N538K and E540D consistently conferred resistance to moxifloxacin only. Transductants and clinical isolates harboring T539N, T539P or N538T+T546M mutations exhibited low-level resistance to moxifloxacin only but not consistently. These findings indicate that certain mutations in gyrB confer fluoroquinolone resistance, but the level and pattern of resistance varies among the different mutations. The results from this study provide support for the inclusion of the QRDR of gyrB in molecular assays used to detect fluoroquinolone resistance in M. tuberculosis.
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Affiliation(s)
- Seidu Malik
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Melisa Willby
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - David Sikes
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Oleg V. Tsodikov
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, United States of America
| | - James E. Posey
- Laboratory Branch, Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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26
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Hong S, Cheng TY, Layre E, Sweet L, Young DC, Posey JE, Butler WR, Moody DB. Ultralong C100 mycolic acids support the assignment of Segniliparus as a new bacterial genus. PLoS One 2012; 7:e39017. [PMID: 22720018 PMCID: PMC3375245 DOI: 10.1371/journal.pone.0039017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 05/15/2012] [Indexed: 11/19/2022] Open
Abstract
Mycolic acid-producing bacteria isolated from the respiratory tract of human and non-human mammals were recently assigned as a distinct genus, Segniliparus, because they diverge from rhodococci and mycobacteria in genetic and chemical features. Using high accuracy mass spectrometry, we determined the chemical composition of 65 homologous mycolic acids in two Segniliparus species and separately analyzed the three subclasses to measure relative chain length, number and stereochemistry of unsaturations and cyclopropyl groups within each class. Whereas mycobacterial mycolate subclasses are distinguished from one another by R groups on the meromycolate chain, Segniliparus species synthesize solely non-oxygenated α-mycolates with high levels of cis unsaturation. Unexpectedly Segniliparus α-mycolates diverge into three subclasses based on large differences in carbon chain length with one bacterial culture producing mycolates that range from C58 to C100. Both the overall chain length (C100) and the chain length diversity (C42) are larger than previously seen for mycolic acid-producing organisms and provide direct chemical evidence for assignment of Segniliparus as a distinct genus. Yet, electron microscopy shows that the long and diverse mycolates pack into a typical appearing membrane. Therefore, these new and unexpected extremes of mycolic acid chemical structure raise questions about the modes of mycolic acid packing and folding into a membrane.
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Affiliation(s)
- Sunhee Hong
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tan-Yun Cheng
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Emilie Layre
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lindsay Sweet
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - David C. Young
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - James E. Posey
- Division of Tuberculosis Elimination, National Center for HIV, STD and Tuberculosis Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - W. Ray Butler
- Division of Tuberculosis Elimination, National Center for HIV, STD and Tuberculosis Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail: (DBM); (WRB)
| | - D. Branch Moody
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (DBM); (WRB)
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27
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Weiner B, Gomez J, Victor TC, Warren RM, Sloutsky A, Plikaytis BB, Posey JE, van Helden PD, Gey van Pittius NC, Koehrsen M, Sisk P, Stolte C, White J, Gagneux S, Birren B, Hung D, Murray M, Galagan J. Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region. PLoS One 2012; 7:e26038. [PMID: 22347359 PMCID: PMC3274525 DOI: 10.1371/journal.pone.0026038] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 09/16/2011] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium tuberculosis, the causative agent of most human tuberculosis, infects one third of the world's population and kills an estimated 1.7 million people a year. With the world-wide emergence of drug resistance, and the finding of more functional genetic diversity than previously expected, there is a renewed interest in understanding the forces driving genome evolution of this important pathogen. Genetic diversity in M. tuberculosis is dominated by single nucleotide polymorphisms and small scale gene deletion, with little or no evidence for large scale genome rearrangements seen in other bacteria. Recently, a single report described a large scale genome duplication that was suggested to be specific to the Beijing lineage. We report here multiple independent large-scale duplications of the same genomic region of M. tuberculosis detected through whole-genome sequencing. The duplications occur in strains belonging to both M. tuberculosis lineage 2 and 4, and are thus not limited to Beijing strains. The duplications occur in both drug-resistant and drug susceptible strains. The duplicated regions also have substantially different boundaries in different strains, indicating different originating duplication events. We further identify a smaller segmental duplication of a different genomic region of a lab strain of H37Rv. The presence of multiple independent duplications of the same genomic region suggests either instability in this region, a selective advantage conferred by the duplication, or both. The identified duplications suggest that large-scale gene duplication may be more common in M. tuberculosis than previously considered.
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Affiliation(s)
- Brian Weiner
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - James Gomez
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Thomas C. Victor
- Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Health Sciences, National Research Foundation Centre of Excellence for Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, South Africa
| | - Robert M. Warren
- Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Health Sciences, National Research Foundation Centre of Excellence for Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, South Africa
| | - Alexander Sloutsky
- Massachusetts Supranational TB Reference Laboratory, Center for Health Policy and Research, University of Massachusetts Medical School, Shrewsbury, Massachusetts, United States of America
| | - Bonnie B. Plikaytis
- Mycobacteriology Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - James E. Posey
- Mycobacteriology Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Paul D. van Helden
- Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Health Sciences, National Research Foundation Centre of Excellence for Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, South Africa
| | - Nicolass C. Gey van Pittius
- Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Health Sciences, National Research Foundation Centre of Excellence for Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, South Africa
| | - Michael Koehrsen
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Peter Sisk
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Christian Stolte
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Jared White
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Sebastien Gagneux
- Medical Research Council, National Institute for Medical Research, London, United Kingdom
| | - Bruce Birren
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Deborah Hung
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Megan Murray
- Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - James Galagan
- The Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Biomedical Engineering and Microbiology, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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28
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Sable SB, Cheruvu M, Nandakumar S, Sharma S, Bandyopadhyay K, Kellar KL, Posey JE, Plikaytis BB, Amara RR, Shinnick TM. Cellular immune responses to nine Mycobacterium tuberculosis vaccine candidates following intranasal vaccination. PLoS One 2011; 6:e22718. [PMID: 21799939 PMCID: PMC3143185 DOI: 10.1371/journal.pone.0022718] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 06/29/2011] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The identification of Mycobacterium tuberculosis vaccines that elicit a protective immune response in the lungs is important for the development of an effective vaccine against tuberculosis. METHODS AND PRINCIPAL FINDINGS In this study, a comparison of intranasal (i.n.) and subcutaneous (s.c.) vaccination with the BCG vaccine demonstrated that a single moderate dose delivered intranasally induced a stronger and sustained M. tuberculosis-specific T-cell response in lung parenchyma and cervical lymph nodes of BALB/c mice than vaccine delivered subcutaneously. Both BCG and a multicomponent subunit vaccine composed of nine M. tuberculosis recombinant proteins induced strong antigen-specific T-cell responses in various local and peripheral immune compartments. Among the nine recombinant proteins evaluated, the alanine proline rich antigen (Apa, Rv1860) was highly antigenic following i.n. BCG and immunogenic after vaccination with a combination of the nine recombinant antigens. The Apa-induced responses included induction of both type 1 and type 2 cytokines in the lungs as evaluated by ELISPOT and a multiplexed microsphere-based cytokine immunoassay. Of importance, i.n. subunit vaccination with Apa imparted significant protection in the lungs and spleen of mice against M. tuberculosis challenge. Despite observed differences in the frequencies and location of specific cytokine secreting T cells both BCG vaccination routes afforded comparable levels of protection in our study. CONCLUSION AND SIGNIFICANCE Overall, our findings support consideration and further evaluation of an intranasally targeted Apa-based vaccine to prevent tuberculosis.
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Affiliation(s)
- Suraj B Sable
- Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America.
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Hiraishi Y, Nandakumar S, Choi SO, Lee JW, Kim YC, Posey JE, Sable SB, Prausnitz MR. Bacillus Calmette-Guérin vaccination using a microneedle patch. Vaccine 2011; 29:2626-36. [PMID: 21277407 DOI: 10.1016/j.vaccine.2011.01.042] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 01/15/2011] [Accepted: 01/17/2011] [Indexed: 11/16/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis continues to be a leading cause of mortality among bacterial diseases, and the bacillus Calmette-Guérin (BCG) is the only licensed vaccine for human use against this disease. TB prevention and control would benefit from an improved method of BCG vaccination that simplifies logistics and eliminates dangers posed by hypodermic needles without compromising immunogenicity. Here, we report the design and engineering of a BCG-coated microneedle vaccine patch for a simple and improved intradermal delivery of the vaccine. The microneedle vaccine patch induced a robust cell-mediated immune response in both the lungs and the spleen of guinea pigs. The response was comparable to the traditional hypodermic needle based intradermal BCG vaccination and was characterized by a strong antigen specific lymphocyte proliferation and IFN-γ levels with high frequencies of CD4(+)IFN-γ(+), CD4(+)TNF-α(+) and CD4(+)IFN-γ(+)TNF-α(+) T cells. The BCG-coated microneedle vaccine patch was highly immunogenic in guinea pigs and supports further exploration of this new technology as a simpler, safer, and compliant vaccination that could facilitate increased coverage, especially in developing countries that lack adequate healthcare infrastructure.
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Affiliation(s)
- Yasuhiro Hiraishi
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive, N.W., Atlanta, GA 30332, USA
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Abstract
The twin-arginine translocation (TAT) system secretes fully folded proteins that contain a twin-arginine motif within their signal sequence across the cytoplasmic membrane in bacteria. Using a green fluorescent protein fused with a TAT signal sequence, we demonstrated that Mycobacterium smegmatis contains a TAT system. By inactivating individual genes, we showed that three genes (tatA, tatB, and tatC) are required for a functional TAT system in M. smegmatis. The tat mutants exhibited a decreased growth rate and altered colony morphology compared to the parent strain. Comparison of the secreted proteins of the deltatatC and parent strain by two-dimensional polyacrylamide gel electrophoresis revealed an alteration in the secretion of at least five proteins, and one of the major TAT-dependent secreted proteins was identified as beta-lactamase (BlaS). The genome of M. smegmatis was analyzed with the TATFIND program, and 49 putative TAT substrates were identified, including the succinate transporter DctP. Because disruption of the TAT secretion system has a direct effect on the physiology of M. smegmatis and homologs of the TAT proteins are also present in the genome of Mycobacterium tuberculosis, the TAT secretion system or its substrates may be good candidates for drug or vaccine development.
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Affiliation(s)
- James E Posey
- Division of TB Elimination, National Center for HIV, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
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Boylan JA, Posey JE, Gherardini FC. Borrelia oxidative stress response regulator, BosR: a distinctive Zn-dependent transcriptional activator. Proc Natl Acad Sci U S A 2003; 100:11684-9. [PMID: 12975527 PMCID: PMC208818 DOI: 10.1073/pnas.2032956100] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability of a pathogen to cause infection depends on successful colonization of the host, which, in turn, requires adaptation to various challenges presented by that host. For example, host immune cells use a variety of mechanisms to control infection by bacterial pathogens, including the production of bactericidal reactive oxygen species. Prokaryotic and eukaryotic cells have developed ways of protecting themselves against this oxidative damage; for instance, Borrelia burgdorferi alters the expression of oxidative-stress-related proteins, such as a Dps/Dpr homolog NapA (BB0690), in response to increasing levels of oxygen and reactive oxygen species. These stress-related genes appear to be regulated by a putative metal-dependent DNA-binding protein (BB0647) that has 50.7% similarity to the peroxide-specific stress response repressor of Bacillus subtilis, PerR. We overexpressed and purified this protein from Escherichia coli and designated it Borrelia oxidative stress regulator, BosR. BosR bound to a 50-nt region 180 bp upstream of the napA transcriptional start site and required DTT and Zn2+ for optimal binding. Unlike the Bacillus subtilis PerR repressor, BosR did not require Fe2+ and Mn2+ for binding, and oxidizing agents, such as t-butyl peroxide, enhanced, not eliminated, BosR binding to the napA promoter region. Surprisingly, transcriptional fusion analysis indicated that BosR exerted a positive regulatory effect on napA that is inducible with t-butyl peroxide. On the basis of these data, we propose that, despite the similarity to PerR, BosR functions primarily as a transcriptional activator, not a repressor of oxidative stress response, in B. burgdorferi.
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Affiliation(s)
- Julie A Boylan
- Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 904 South 4th Street, Hamilton, MT 59840, USA
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Benoit S, Posey JE, Chenoweth MR, Gherardini FC. Treponema pallidum 3-phosphoglycerate mutase is a heat-labile enzyme that may limit the maximum growth temperature for the spirochete. J Bacteriol 2001; 183:4702-8. [PMID: 11466272 PMCID: PMC99523 DOI: 10.1128/jb.183.16.4702-4708.2001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2001] [Accepted: 05/31/2001] [Indexed: 11/20/2022] Open
Abstract
In the causative agent of syphilis, Treponema pallidum, the gene encoding 3-phosphoglycerate mutase, gpm, is part of a six-gene operon (tro operon) that is regulated by the Mn-dependent repressor TroR. Since substrate-level phosphorylation via the Embden-Meyerhof pathway is the principal way to generate ATP in T. pallidum and Gpm is a key enzyme in this pathway, Mn could exert a regulatory effect on central metabolism in this bacterium. To study this, T. pallidum gpm was cloned, Gpm was purified from Escherichia coli, and antiserum against the recombinant protein was raised. Immunoblots indicated that Gpm was expressed in freshly extracted infective T. pallidum. Enzyme assays indicated that Gpm did not require Mn(2+) while 2,3-diphosphoglycerate (DPG) was required for maximum activity. Consistent with these observations, Mn did not copurify with Gpm. The purified Gpm was stable for more than 4 h at 25 degrees C, retained only 50% activity after incubation for 20 min at 34 degrees C or 10 min at 37 degrees C, and was completely inactive after 10 min at 42 degrees C. The temperature effect was attenuated when 1 mM DPG was added to the assay mixture. The recombinant Gpm from pSLB2 complemented E. coli strain PL225 (gpm) and restored growth on minimal glucose medium in a temperature-dependent manner. Increasing the temperature of cultures of E. coli PL225 harboring pSLB2 from 34 to 42 degrees C resulted in a 7- to 11-h period in which no growth occurred (compared to wild-type E. coli). These data suggest that biochemical properties of Gpm could be one contributing factor to the heat sensitivity of T. pallidum.
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Affiliation(s)
- S Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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Abstract
A fundamental tenet of microbial pathogenesis is that bacterial pathogens must overcome host iron limitation to establish a successful infection. Surprisingly, the Lyme disease pathogen Borrelia burgdorferi has bypassed this host defense by eliminating the need for iron. B. burgdorferi grew normally and did not alter gene expression in the presence of iron chelators. Furthermore, typical bacterial iron-containing proteins were not detected in cell lysates, nor were the genes encoding such proteins identified in the genome sequence. The intracellular concentration of iron in B. burgdorferi was estimated to be less than 10 atoms per cell, well below a physiologically relevant concentration.
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Affiliation(s)
- J E Posey
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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Posey JE, Hardham JM, Norris SJ, Gherardini FC. Characterization of a manganese-dependent regulatory protein, TroR, from Treponema pallidum. Proc Natl Acad Sci U S A 1999; 96:10887-92. [PMID: 10485921 PMCID: PMC17978 DOI: 10.1073/pnas.96.19.10887] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome sequence analysis of Treponema pallidum, the causative agent of syphilis, suggests that this bacterium has a limited iron requirement with few, if any, proteins that require iron. Instead, T. pallidum may use manganese-dependent enzymes for metabolic pathways. This strategy apparently alleviates the necessity of T. pallidum to acquire iron from the host, thus overcoming iron limitation, which is a primary host defense. Interestingly, a putative metal-dependent regulatory protein, TroR, which has homology with the diphtheria toxin regulatory protein, DtxR, from Corynebacterium diphtheriae was identified from T. pallidum. We describe here the characterization of TroR, a regulatory protein. Mobility-shift DNA binding and DNase I footprint assays indicated that purified TroR bound to a 22-nt region of dyad symmetry that overlaps the -10 region of the promoter of the tro operon, which contains the genes for a putative metal transport system, the glycolytic enzyme phosphoglycerate mutase, and TroR. Unlike other metal-dependent regulatory proteins like diphtheria toxin regulatory protein and the ferric ion uptake regulator, Fur, which can be activated by divalent metals such as Fe(2+), Mn(2+), Co(2+), Ni(2+), and Zn(2+), TroR is activated only by Mn(2+). The TroR-Mn(2+) complex binds its target sequence and blocks transcription of the troPO/lacZ fusion, suggesting that TroR acts as a metal-dependent repressor in vivo. In addition, TroR exists as a dimer in both its inactive (metal free) and active states as indicated by chemical crosslinking experiments. Based on these data, we propose that TroR represents a unique regulatory system for controlling gene expression in T. pallidum in response to Mn(2+).
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Affiliation(s)
- J E Posey
- The Department of Microbiology, The University of Georgia, Athens, GA 30602, USA
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Ma JF, Ochsner UA, Klotz MG, Nanayakkara VK, Howell ML, Johnson Z, Posey JE, Vasil ML, Monaco JJ, Hassett DJ. Bacterioferritin A modulates catalase A (KatA) activity and resistance to hydrogen peroxide in Pseudomonas aeruginosa. J Bacteriol 1999; 181:3730-42. [PMID: 10368148 PMCID: PMC93851 DOI: 10.1128/jb.181.12.3730-3742.1999] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have cloned a 3.6-kb genomic DNA fragment from Pseudomonas aeruginosa harboring the rpoA, rplQ, katA, and bfrA genes. These loci are predicted to encode, respectively, (i) the alpha subunit of RNA polymerase; (ii) the L17 ribosomal protein; (iii) the major catalase, KatA; and (iv) one of two iron storage proteins called bacterioferritin A (BfrA; cytochrome b1 or b557). Our goal was to determine the contributions of KatA and BfrA to the resistance of P. aeruginosa to hydrogen peroxide (H2O2). When provided on a multicopy plasmid, the P. aeruginosa katA gene complemented a catalase-deficient strain of Escherichia coli. The katA gene was found to contain two translational start codons encoding a heteromultimer of approximately 160 to 170 kDa and having an apparent Km for H2O2 of 44.7 mM. Isogenic katA and bfrA mutants were hypersusceptible to H2O2, while a katA bfrA double mutant demonstrated the greatest sensitivity. The katA and katA bfrA mutants possessed no detectable catalase activity. Interestingly, a bfrA mutant expressed only approximately 47% the KatA activity of wild-type organisms, despite possessing wild-type katA transcription and translation. Plasmids harboring bfrA genes encoding BfrA altered at critical amino acids essential for ferroxidase activity could not restore wild-type catalase activity in the bfrA mutant. RNase protection assays revealed that katA and bfrA are on different transcripts, the levels of which are increased by both iron and H2O2. Mass spectrometry analysis of whole cells revealed no significant difference in total cellular iron levels in the bfrA, katA, and katA bfrA mutants relative to wild-type bacteria. Our results suggest that P. aeruginosa BfrA may be required as one source of iron for the heme prosthetic group of KatA and thus for protection against H2O2.
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Affiliation(s)
- J F Ma
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267-0524, USA
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