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Cernicchi G, Rampacci E, Massari S, Manfroni G, Barreca ML, Tabarrini O, Cecchetti V, Felicetti T, Di Luca M, Poma NV, Tavanti A, Passamonti F, Rindi L, Sabatini S. Discovery of 2-phenylquinazolines as potent Mycobacterium avium efflux pump inhibitors able to synergize with clarithromycin against clinical isolate. Arch Pharm (Weinheim) 2024; 357:e2400296. [PMID: 38923553 DOI: 10.1002/ardp.202400296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Nontuberculous mycobacteria (NTM), which include the Mycobacterium avium complex, are classified as difficult-to-treat pathogens due to their ability to quickly develop drug resistance against the most common antibiotics used to treat NTM infections. The overexpression of efflux pumps (EPs) was demonstrated to be a key mechanism of clarithromycin (CLA) resistance in NTM. Therefore, in this work, 24 compounds from an in-house library, characterized by chemical diversity, were tested as potential NTM EP inhibitors (EPIs) against Mycobacterium smegmatis mc2 155 and M. avium clinical isolates. Based on the acquired results, 12 novel analogs of the best derivatives 1b and 7b were designed and synthesized to improve the NTM EP inhibition activity. Among the second set of compounds, 13b emerged as the most potent NTM EPI. At a concentration of 4 µg/mL, it reduced the CLA minimum inhibitory concentration by 16-fold against the clinical isolate M. avium 2373 overexpressing EPs as primary mechanism of CLA resistance.
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Affiliation(s)
- Giada Cernicchi
- Department Pharmaceutical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Elisa Rampacci
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - Serena Massari
- Department Pharmaceutical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Giuseppe Manfroni
- Department Pharmaceutical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Maria Letizia Barreca
- Department Pharmaceutical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Oriana Tabarrini
- Department Pharmaceutical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Violetta Cecchetti
- Department Pharmaceutical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | - Tommaso Felicetti
- Department Pharmaceutical Sciences, Università degli Studi di Perugia, Perugia, Italy
| | | | | | | | | | - Laura Rindi
- Department of Translational Research and New Technologies in Medicine and Surgery, Università di Pisa, Pisa, Italy
| | - Stefano Sabatini
- Department Pharmaceutical Sciences, Università degli Studi di Perugia, Perugia, Italy
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Deshpande D, Srivastava S, Gumbo T. Ertapenem's therapeutic potential for Mycobacterium avium lung disease in the hollow fibre model. Int J Antimicrob Agents 2024; 64:107204. [PMID: 38754528 PMCID: PMC11371482 DOI: 10.1016/j.ijantimicag.2024.107204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 04/25/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION Guideline-based therapy for Mycobacterium avium complex (MAC) pulmonary disease achieves sustained sputum conversion rates in only 43-53% of patients. Repurposing of β-lactam antibiotics such as ertapenem could expedite design of more efficacious regimens, compared to developing new drugs. METHODS We performed an ertapenem exposure-response study in the hollow fibre system model of intracellular MAC (HFS-MAC). We recapitulated human-like intrapulmonary concentration-time profiles of eight once-daily intravenous doses of ertapenem over 28 days and performed repetitive sampling for drug concentration-time profiles and MAC burden. The % of time concentration persisted above MIC (%TMIC) mediating either 50% or 80% of maximal effect (E50, EC80) were identified. The EC80 was used as target exposure in a 10 000 subject Monte Carlo experiments for ertapenem doses of 1G, 2G, or 4G administered once versus twice daily. RESULTS The ertapenem MIC ranged from 0.5 to 2 mg/L on three occasions. Ertapenem achieved a half-life of 4.04 ± 0.80 h in the HFS-MAC and killed a maximum of 2.17 log10 CFU/mL below day 0. The EC50 was %TMIC of 75.9% (95% confidence interval: 68.43%-86.54%) and the EC80 was %TMIC of 100%. Target attainment probability was >90% for 1G twice daily up to an MIC of 2 mg/L, while for 2G twice daily the susceptibility MIC breakpoint was 4-8 mg/L. CONCLUSIONS Ertapenem microbial kill below day 0 burden was better than guideline-based therapy drugs in the HFS-MAC in the past. Ertapenem is a promising drug for novel combination therapies for MAC lung disease.
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Affiliation(s)
| | - Shashikant Srivastava
- Department of Medicine, School of Medicine, the University of Texas at Tyler, Tyler, Texas, USA; Department of Cellular and Molecular Biology, Center for Biomedical Research, University of Texas Health Science Center, Tyler, Texas, USA
| | - Tawanda Gumbo
- Hollow Fiber System & Experimental Therapeutics Laboratories, Irving, Texas, USA; Mathematical Modeling and AI Department, Praedicare Inc., Irving, Texas, USA.
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Deshpande D, Magombedze G, Boorgula GD, Chapagain M, Srivastava S, Gumbo T. Ceftriaxone Efficacy for Mycobacterium avium Complex Lung Disease in the Hollow Fiber and Translation to Sustained Sputum Culture Conversion in Patients. J Infect Dis 2024; 230:e230-e240. [PMID: 38036299 PMCID: PMC11326821 DOI: 10.1093/infdis/jiad545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/17/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Only 35.6%-50.8% of patients with Mycobacterium avium complex (MAC) pulmonary disease achieve sustained sputum culture conversion (SSCC) on treatment with the azithromycin-ethambutol-rifabutin standard of care (SOC). We tested the efficacy of ceftriaxone, a β-lactam with a lung-to-serum penetration ratio of 12.18-fold. METHODS We mimicked lung concentration-time profiles of 7 ceftriaxone once-daily doses for 28 days in the hollow fiber system model of intracellular MAC (HFS-MAC). Monte Carlo experiments were used for dose selection. We also compared once-daily ceftriaxone monotherapy to 3-drug SOC against 5 MAC clinical isolates in HFS-MAC using γ (kill) slopes, and translated to SSCC rates. RESULTS Ceftriaxone killed 1.02-3.82 log10 colony-forming units (CFU)/mL, at optimal dose of 2 g once-daily. Ceftriaxone killed all 5 strains below day 0 versus 2 of 5 for SOC. The median γ (95% confidence interval [CI]) was 0.49 (.47-.52) log10 CFU/mL/day for ceftriaxone and 0.38 (.34-.43) log10 CFU/mL/day for SOC. In patients, the SOC was predicted to achieve SSCC rates (CI) of 39.3% (36%-42%) at 6 months. The SOC SSCC was 50% at 8.18 (3.64-27.66) months versus 3.58 (2.20-7.23) months for ceftriaxone, shortening time to SSCC 2.35-fold. CONCLUSIONS Ceftriaxone is a promising agent for creation of short-course chemotherapy.
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Affiliation(s)
| | | | | | - Moti Chapagain
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas Health Science Center at Tyler
| | - Shashikant Srivastava
- Baylor University Medical Center, Dallas
- Department of Medicine, School of Medicine, University of Texas at Tyler
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas Health Science Center at Tyler
| | - Tawanda Gumbo
- Mathematical Modeling and AI Department, Praedicare Inc, Dallas
- Hollow Fiber System and Experimental Therapeutics Laboratories, Praedicare Inc, Dallas, Texas
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Akanksha, Mehra S. Conserved Evolutionary Trajectory Can Be Perturbed to Prevent Resistance Evolution under Norfloxacin Pressure by Forcing Mycobacterium smegmatis on Alternate Evolutionary Paths. ACS Infect Dis 2024; 10:2623-2636. [PMID: 38959403 DOI: 10.1021/acsinfecdis.3c00605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
Antibiotic resistance is a pressing health issue, with the emergence of resistance in bacteria outcompeting the discovery of novel drug candidates. While many studies have used Adaptive Laboratory Evolution (ALE) to understand the determinants of resistance, the influence of the drug dosing profile on the evolutionary trajectory remains understudied. In this study, we employed ALE on Mycobacterium smegmatis exposed to various concentrations of Norfloxacin using both cyclic constant and stepwise increasing drug dosages to examine their impact on the resistance mechanisms selected. Mutations in an efflux pump regulator, LfrR, were found in all of the evolved populations irrespective of the drug profile and population bottleneck, indicating a conserved efflux-based resistance mechanism. This mutation appeared early in the evolutionary trajectory, providing low-level resistance when present alone, with a further increase in resistance resulting from successive accumulation of other mutations. Notably, drug target mutations, similar to those observed in clinical isolates, were only seen above a threshold of greater than 4× the minimum inhibitory concentration (MIC). A combination of three mutations in the genes, lfrR, MSMEG_1959, and MSMEG_5045, was conserved across multiple lineages, leading to high-level resistance and preceding the appearance of drug target mutations. Interestingly, in populations evolved from parental strains lacking the lfrA efflux pump, the primary target of the lfrR regulator, no lfrR gene mutations are selected. Furthermore, evolutional trajectories originating from the ΔlfrA strain displayed early arrest in some lineages and the absence of target gene mutations in those that evolved, albeit delayed. Thus, blocking or inhibiting the expression of efflux pumps can arrest or delay the fixation of drug target mutations, potentially limiting the maximum attainable resistance levels.
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Affiliation(s)
- Akanksha
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Sarika Mehra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
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Roberts AH, Moon CW, Faulkner V, Kendall SL, Waddell SJ, Bacon J. EfpA is required for regrowth of Mycobacterium tuberculosis following isoniazid exposure. Antimicrob Agents Chemother 2024; 68:e0026124. [PMID: 39037241 PMCID: PMC11304720 DOI: 10.1128/aac.00261-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/02/2024] [Indexed: 07/23/2024] Open
Abstract
Efflux of antibiotics is an important survival strategy in bacteria. Mycobacterium tuberculosis has approximately sixty efflux pumps, but little is known about the role of each pump or the substrates they efflux. The putative efflux pump, EfpA, is a member of the major facilitator superfamily and has been shown to be essential by saturation transposon mutagenesis studies. It has been implicated in the efflux of isoniazid (INH), which is a first-line drug used to treat tuberculosis (TB). This is supported by evidence from transcriptional profiling showing that efpA is induced in response to INH exposure. However, its roles in the physiology and adaptation of M. tuberculosis to antibiotics have yet to be determined. In this study, we describe the repression of efpA in M. tuberculosis, using CRISPR interference (CRISPRi) to knockdown the expression of this essential gene and the direct effect of this on the ability of M. tuberculosis to survive exposure to INH over a 45-day time course. We determined that wild-type levels of efpA were required for recovery of M. tuberculosis following INH exposure and that, after 45 days of INH exposure, only a few viable colonies were recoverable from efpA-repressed M. tuberculosis. We conclude that EfpA is required for recovery of M. tuberculosis following INH exposure, which could reduce the efficacy of INH in vivo, and that EfpA may have a role in the development of resistance during drug therapy.
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Affiliation(s)
- Adam H. Roberts
- Discovery Group, VDEC, UK Health Security Agency, Porton Down, Salisbury, United Kingdom
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Christopher W. Moon
- Discovery Group, VDEC, UK Health Security Agency, Porton Down, Salisbury, United Kingdom
| | - Valwynne Faulkner
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Sharon L. Kendall
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, United Kingdom
| | - Simon J. Waddell
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Joanna Bacon
- Discovery Group, VDEC, UK Health Security Agency, Porton Down, Salisbury, United Kingdom
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Deshpande D, Magombedze G, Srivastava S, Gumbo T. Antibacterial action of penicillin against Mycobacterium avium complex. IJTLD OPEN 2024; 1:362-368. [PMID: 39131587 PMCID: PMC11308404 DOI: 10.5588/ijtldopen.24.0238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Accepted: 07/11/2024] [Indexed: 08/13/2024]
Abstract
INTRODUCTION β-lactam antibiotics are promising treatments for Mycobacterium avium complex (MAC) lung disease. We hypothesized that benzylpenicillin has efficacy against MAC. METHODS Benzylpenicillin lung concentration-time profiles of seven doses in three dosing schedules were administered for 28 days using the hollow fiber system model of intracellular MAC (HFS-MAC). Data were analyzed using the inhibitory sigmoid maximal effect (Emax) model for each sampling day, while two ordinary differential equations (ODEs) were used for the wild-type and penicillin-resistant mutants. RESULTS Benzylpenicillin killed >2.1 log10 colony-forming unit (CFU)/mL below Day 0, better than azithromycin, ethambutol, and rifabutin. Efficacy was terminated by acquired resistance. Sigmoid Emax parameter estimates significantly differed between sampling days and were a poor fit. However, ODE model parameter estimates vs. exposure were a better fit. The exposure mediating Emax was 84.6% (95% CI 76.91-82.98) of time concentration exceeded the minimum inhibitory concentration (MIC). In Monte Carlo experiments, 24 million international units of benzylpenicillin continuous infusion achieved the target exposure in lungs of >90% of 10,000 subjects until an MIC of 64 mg/L, designated the susceptibility breakpoint. CONCLUSIONS Benzylpenicillin demonstrated a better bactericidal effect against MAC than guideline-recommended drugs before the development of resistance. Its role in combination therapy with other drugs with better efficacy than guideline-recommended drugs should be explored.
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Affiliation(s)
- D Deshpande
- Baylor University Medical Center, Dallas, TX, USA
| | - G Magombedze
- Mathematical Modeling and AI Department, Praedicare Inc, Dallas, TX, USA
| | - S Srivastava
- Department of Medicine, School of Medicine, University of Texas at Tyler, Tyler, TX, USA
- Department of Cellular and Molecular Biology, Center for Biomedical Research, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - T Gumbo
- Mathematical Modeling and AI Department, Praedicare Inc, Dallas, TX, USA
- Hollow Fiber System & Experimental Therapeutics Laboratories, Praedicare Inc, Dallas, Texas, USA
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Shyam M, Kumar S, Singh V. Unlocking Opportunities for Mycobacterium leprae and Mycobacterium ulcerans. ACS Infect Dis 2024; 10:251-269. [PMID: 38295025 PMCID: PMC10862552 DOI: 10.1021/acsinfecdis.3c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 02/02/2024]
Abstract
In the recent decade, scientific communities have toiled to tackle the emerging burden of drug-resistant tuberculosis (DR-TB) and rapidly growing opportunistic nontuberculous mycobacteria (NTM). Among these, two neglected mycobacteria species of the Acinetobacter family, Mycobacterium leprae and Mycobacterium ulcerans, are the etiological agents of leprosy and Buruli ulcer infections, respectively, and fall under the broad umbrella of neglected tropical diseases (NTDs). Unfortunately, lackluster drug discovery efforts have been made against these pathogenic bacteria in the recent decade, resulting in the discovery of only a few countable hits and majorly repurposing anti-TB drug candidates such as telacebec (Q203), P218, and TB47 for current therapeutic interventions. Major ignorance in drug candidate identification might aggravate the dramatic consequences of rapidly spreading mycobacterial NTDs in the coming days. Therefore, this Review focuses on an up-to-date account of drug discovery efforts targeting selected druggable targets from both bacilli, including the accompanying challenges that have been identified and are responsible for the slow drug discovery. Furthermore, a succinct discussion of the all-new possibilities that could be alternative solutions to mitigate the neglected mycobacterial NTD burden and subsequently accelerate the drug discovery effort is also included. We anticipate that the state-of-the-art strategies discussed here may attract major attention from the scientific community to navigate and expand the roadmap for the discovery of next-generation therapeutics against these NTDs.
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Affiliation(s)
- Mousumi Shyam
- Department
of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mersa, Ranchi, Jharkhand 835215, India
| | - Sumit Kumar
- Holistic
Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa
| | - Vinayak Singh
- Holistic
Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch 7701, South Africa
- South
African Medical Research Council Drug Discovery and Development Research
Unit, University of Cape Town, Rondebosch 7701, South Africa
- Institute
of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Observatory 7925, Cape Town, South Africa
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Farnia P, Besharati S, Farina P, Ayoubi S, Marjani M, Ghanavi J, Tabarsi P, Velayati AA. The Role of Efflux Pumps transporter in Multi-drug Resistant Tuberculosis: Mycobacterial memberane protein(MmpL5). Int J Mycobacteriol 2024; 13:7-14. [PMID: 38771273 DOI: 10.4103/ijmy.ijmy_37_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/04/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND The overexpression of efflux pumps (Eps) was reported to contribute to multidrug resistant tuberculosis (MDR-TB). Increases in Eps that expel structurally unrelated drugs contribute to reduced susceptibility by decreasing the intracellular concentration of antibiotics. In the present study, an association of mycobacterial membrane protein (MmpS5-MmpL5) Ep and its gene regulator (Rv0678) was investigated in MDR-tuberculosis isolates. METHODS MTB strains were isolated from patients at two different intervals, i.e., once when they had persistent symptoms despite 3-15 ≥ months of treatment and once when they had started new combination therapy ≥2-3 months. Sputum specimens were subjected to Xpert MTB/rifampicin test and then further susceptibility testing using proportional method and multiplex polymerase chain reaction (PCR) were performed on them. The isolates were characterized using both 16S-23S RNA and hsp65 genes spacer (PCR-restriction fragment length polymorphism). Whole-genome sequencing (WGS) was investigated on two isolates from culture-positive specimen per patient. The protein structure was simulated using the SWISS-MODEL. The input format used for this web server was FASTA (amino acid sequence). Protein structure was also analysis using Ramachandran plot. RESULTS WGS documented deletion, insertion, and substitution in transmembrane transport protein MmpL5 (Rv0676) of Eps. Majority of the studied isolates (n = 12; 92.3%) showed a unique deletion mutation at three positions: (a) from amino acid number 771 (isoleucine) to 776 (valine), (b) from amino acid number 785 (valine) to 793 (histidine), and (c) from amino acid number 798 (leucine) to 806 (glycine)." One isolate (7.6%) had no deletion mutation. In all isolates (n = 13; 100%), a large insertion mutation consisting of 94 amino acid was observed "from amino acid number 846 (isoleucine) to amino acid number 939 (leucine)". Thirty-eight substitutions in Rv0676 were detected, of which 92.3% were identical in the studied isolates. WGS of mycobacterial membrane proteins (MmpS5; Rv0677) and its gene regulator (Rv0678) documented no deletion, insertion, and substitution. No differences were observed between MmpS5-MmpL5 and its gene regulator in isolates that were collected at different intervals. CONCLUSIONS Significant genetic mutation like insertion, deletion, and substitution within transmembrane transport protein MmpL5 (Rv0676) can change the functional balance of Eps and cause a reduction in drug susceptibility. This is the first report documenting a unique amino acid mutation (insertion and deletion ≥4-94) in Rv0676 among drug-resistant MTB. We suggest the changes in Mmpl5 (Rv0676) might occurred due to in-vivo sub-therapeutic drug stress within the host cell. Changes in MmpL5 are stable and detected through subsequent culture-positive specimens.
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Affiliation(s)
- Parissa Farnia
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeid Besharati
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Poopak Farina
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saman Ayoubi
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Marjani
- Clinical Tuberculosis and Epidemiology Research Centre, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jalaledin Ghanavi
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Payam Tabarsi
- Clinical Tuberculosis and Epidemiology Research Centre, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Akbar Velayati
- Mycobacteriology Research Center, National Research Institute of Tuberculosis and Lung Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Kamala K, Sivaperumal P. Prevalence of enterotoxin genes of Staphylococcus sp. isolated from marine fish to reveal seafood contamination. MARINE POLLUTION BULLETIN 2023; 195:115464. [PMID: 37666137 DOI: 10.1016/j.marpolbul.2023.115464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/22/2023] [Accepted: 08/26/2023] [Indexed: 09/06/2023]
Abstract
Seafood is a valuable nutritional source, but it is highly susceptible to bacterial contamination, posing a severe health risk to humans. Enterotoxin-producing genes carrying Staphylococcus sp. are a significant concern in marine fish. This study aimed to investigate the prevalence of enterotoxin genes in Staphylococcus sp. isolated from 17 common fish species and emphasise the need for improving seafood quality and hygiene. The potential risks of contamination by enterotoxin-producing Staphylococcus sp. were assessed. The results indicated the risk associated with the consumption of contaminated seafood, especially from marketed and frozen samples. Gene expression analysis on a heat map revealed that samples stored in markets are heavily loaded with Staphylococcus enterotoxin genes due to the unhygienic water that was used from the local markets for fish processing. To enhance seafood quality, effective measures on handling and storage should be regularly monitored, and they must be implemented throughout the local seafood markets.
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Affiliation(s)
- Kannan Kamala
- Centre for Marine Actinobacterial Research (CMAR), Department of Physiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Pitchiah Sivaperumal
- Marine Biomedical Research Lab & Environmental Toxicology Unit, Centre for Marine Research and Conservation, Saveetha Dental College and Hospitals, Saveetha Institute of Medical & Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India.
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Loewenstein D, van Balveren L, Lemson A, Hanemaaijer N, Hoefsloot W, van Ingen J. Monotherapy: Key cause of macrolide-resistant Mycobacterium avium complex disease. Respir Med 2023; 217:107366. [PMID: 37481170 DOI: 10.1016/j.rmed.2023.107366] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/03/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023]
Abstract
BACKGROUND Macrolide-resistant Mycobacterium avium complex (MAC) disease is very difficult to cure. Macrolide-resistance emerges in patients and is largely preventable by appropriate screening and treatment practices. METHODS Patients with macrolide-resistant MAC isolates between March 2019 and March 2022 were retrieved from the mycobacteriology reference laboratory database at Radboudumc, Nijmegen, the Netherlands. Clinical consultation reports were extracted from the database to assess the cause of macrolide resistance. RESULTS Sixteen patients with macrolide-resistant MAC disease were included, from a total of 815 patients with MAC isolates (2%); Macrolide monotherapy in bronchiectasis or CF was the most frequent cause of development of macrolide-resistance MAC disease (n = 8; 50%). Short (n = 3; mean duration 9 months, range 6-12) or guideline non-compliant (n = 2) treatment regimens and patient non-adherence (n = 2) were other key causes of macrolide-resistance. CONCLUSIONS Macrolide monotherapy after inappropriate screening is the most frequent cause of macrolide-resistant Mycobacterium avium complex disease in the Netherlands. Educational efforts are needed to prevent this.
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Affiliation(s)
- Daniel Loewenstein
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lars van Balveren
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Arthur Lemson
- Department of Pulmonary Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nicolien Hanemaaijer
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wouter Hoefsloot
- Department of Pulmonary Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, the Netherlands.
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Schildkraut JA, Coolen JPM, Ruesen C, van den Heuvel JJMW, Aceña LE, Wertheim HFL, Jansen RS, Koenderink JB, Te Brake LHM, van Ingen J. The potential role of drug transporters and amikacin modifying enzymes in M. avium. J Glob Antimicrob Resist 2023; 34:161-165. [PMID: 37453496 DOI: 10.1016/j.jgar.2023.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/27/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023] Open
Abstract
OBJECTIVES Mycobacterium avium (M. avium) complex bacteria cause opportunistic infections in humans. Treatment yields cure rates of 60% and consists of a macrolide, a rifamycin, and ethambutol, and in severe cases, amikacin. Mechanisms of antibiotic tolerance remain mostly unknown. Therefore, we studied the contribution of efflux and amikacin modification to antibiotic susceptibility. METHODS We characterised M. avium ABC transporters and studied their expression together with other transporters following exposure to clarithromycin, amikacin, ethambutol, and rifampicin. We determined the effect of combining the efflux pump inhibitors berberine, verapamil and CCCP (carbonyl cyanide m-chlorophenyl hydrazone), to study the role of efflux on susceptibility. Finally, we studied the modification of amikacin by M. avium using metabolomic analysis. RESULTS Clustering shows conservation between M. avium and M. tuberculosis and transporters from most bacterial subfamilies (2-6, 7a/b, 10-12) were found. The largest number of transporter encoding genes was up-regulated after clarithromycin exposure, and the least following amikacin exposure. Only berberine increased the susceptibility to clarithromycin. Finally, because of the limited effect of amikacin on transporter expression, we studied amikacin modification and showed that M. avium, in contrast to M. abscessus, is not able to modify amikacin. CONCLUSION We show that M. avium carries ABC transporters from all major families important for antibiotic efflux, including homologues shown to have affinity for drugs included in treatment. Efflux inhibition in M. avium can increase susceptibility, but this effect is efflux pump inhibitor- and antibiotic-specific. Finally, the lack of amikacin modifying activity in M. avium is important for its activity.
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Affiliation(s)
- Jodie A Schildkraut
- Radboudumc Centre for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, the Netherlands.
| | - Jordy P M Coolen
- Radboudumc Centre for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Carolien Ruesen
- Centre for Epidemiology and Surveillance of Infectious Diseases, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | | | - Laura Edo Aceña
- Radboudumc Centre for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Heiman F L Wertheim
- Radboudumc Centre for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Robert S Jansen
- Department of Microbiology, RIBES, Radboud University, Nijmegen, the Netherlands
| | - Jan B Koenderink
- Department of Pharmacology and toxicology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Lindsey H M Te Brake
- Radboudumc Centre for Infectious Diseases, Department of Pharmacy, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Jakko van Ingen
- Radboudumc Centre for Infectious Diseases, Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, the Netherlands
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12
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van der Heijden YF, Maruri F, Blackman A, Morrison R, Guo Y, Sterling TR. Mycobacterium tuberculosis Gene Expression Associated With Fluoroquinolone Resistance and Efflux Pump Inhibition. J Infect Dis 2023; 228:469-478. [PMID: 37079382 PMCID: PMC10428193 DOI: 10.1093/infdis/jiad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/14/2023] [Accepted: 04/18/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND We evaluated the relationship between response to efflux pump inhibition in fluoroquinolone-resistant Mycobacterium tuberculosis (Mtb) isolates and differences in gene expression and expression quantitative trait loci (eQTL). METHODS We determined ofloxacin minimum inhibitory concentration (MIC) for ofloxacin-resistant and -susceptible Mtb isolates without and with the efflux pump inhibitor verapamil. We performed RNA sequencing (RNA-seq), whole genome sequencing (WGS), and eQTL analysis, focusing on efflux pump, transport, and secretion-associated genes. RESULTS Of 42 ofloxacin-resistant Mtb isolates, 27 had adequate WGS coverage and acceptable RNA-seq quality. Of these 27, 7 had >2-fold reduction in ofloxacin MIC with verapamil; 6 had 2-fold reduction, and 14 had <2-fold reduction. Five genes (including Rv0191) had significantly increased expression in the MIC fold change >2 compared to <2 groups. Among regulated genes, 31 eQTLs (without ofloxacin) and 35 eQTLs (with ofloxacin) had significant allele frequency differences between MIC fold change >2 and <2 groups. Of these, Rv1410c, Rv2459, and Rv3756c (without ofloxacin) and Rv0191 and Rv3756c (with ofloxacin) have previously been associated with antituberculosis drug resistance. CONCLUSIONS In this first reported eQTL analysis in Mtb, Rv0191 had increased gene expression and significance in eQTL analysis, making it a candidate for functional evaluation of efflux-mediated fluoroquinolone resistance in Mtb.
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Affiliation(s)
- Yuri F van der Heijden
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- The Aurum Institute, Johannesburg, South Africa
| | - Fernanda Maruri
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Amondrea Blackman
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Robert Morrison
- Pathogenesis and Immunity Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Yan Guo
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Timothy R Sterling
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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13
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Nagy EZ, Kovács ÁB, Wehmann E, Bekő K, Földi D, Bányai K, Kreizinger Z, Gyuranecz M. Phenotypic and genetic insights into efflux pump mechanism in Mycoplasma anserisalpingitidis. Front Microbiol 2023; 14:1216893. [PMID: 37502405 PMCID: PMC10371760 DOI: 10.3389/fmicb.2023.1216893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023] Open
Abstract
Introduction Mycoplasma anserisalpingitidis is one of the most important waterfowl-pathogenic mycoplasmas. Due to inadequate antibiotic treatment, many strains with high minimal inhibitory concentration (MIC) values for multiple drugs have been isolated lately. Decreased antibiotic susceptibility in several Mycoplasma species are known to be associated with mutations in topoisomerase and ribosomal genes, but other strategies such as active efflux pump mechanisms were also described. The scope of this study was the phenotypic and genetic characterization of the active efflux mechanism in M. anserisalpingitidis. Methods We measured the MIC values in the presence and absence of different efflux pump inhibitors (EPIs), such as carbonyl cyanide m-chlorophenylhydrazine (CCCP), orthovanadate (OV), and reserpine (RSP). Moreover, bioinformatic tools were utilized to detect putative regulatory sequences of membrane transport proteins coding genes, while comparative genome analysis was performed to reveal potential markers of antibiotic resistance. Results Out of the three examined EPIs, CCCP decreased the MICs at least two-fold below the original MICs (in 23 cases out of 36 strains). In the presence of OV or RSP, MIC value differences could be seen only if modified dilution series (10% decrease steps were used instead of two-fold dilutions) were applied (in 24/36 cases with OV and 9/36 with RSP). During comparative genome analysis, non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in genes encoding ABC membrane transport proteins, which were displayed in higher percentages in M. anserisalpingitidis strains with increased MICs. In terms of other genes, a nsSNP was identified in DNA gyrase subunit A (gyrA) gene which can be related to decreased susceptibility to enrofloxacin. The present study is the first to highlight the importance of efflux pump mechanisms in M. anserisalpingitidis. Discussion Considering the observed effects of the EPI CCCP against this bacterium, it can be assumed, that the use of EPIs would increase the efficiency of targeted antibiotic therapy in the future control of this pathogen. However, further research is required to obtain a more comprehensive understanding of efflux pump mechanism in this bacterium.
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Affiliation(s)
- Eszter Zsófia Nagy
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Áron Botond Kovács
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Enikő Wehmann
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Katinka Bekő
- Veterinary Medical Research Institute, Budapest, Hungary
| | - Dorottya Földi
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
| | - Krisztián Bányai
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, Budapest, Hungary
| | - Zsuzsa Kreizinger
- Veterinary Medical Research Institute, Budapest, Hungary
- MolliScience Kft., Biatorbágy, Hungary
| | - Miklós Gyuranecz
- Veterinary Medical Research Institute, Budapest, Hungary
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, Budapest, Hungary
- MolliScience Kft., Biatorbágy, Hungary
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, Budapest, Hungary
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14
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Hamed KA, Tillotson G. A narrative review of nontuberculous mycobacterial pulmonary disease: microbiology, epidemiology, diagnosis, and management challenges. Expert Rev Respir Med 2023; 17:973-988. [PMID: 37962332 DOI: 10.1080/17476348.2023.2283135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023]
Abstract
INTRODUCTION Nontuberculous mycobacteria (NTM) are a diverse group of mycobacterial species that are ubiquitous in the environment. They are opportunistic pathogens that can cause a range of diseases, especially in individuals with underlying structural lung disease or compromised immune systems. AREAS COVERED This paper provides an in-depth analysis of NTM infections, including microbiology, environmental sources and transmission pathways, risk factors for disease, epidemiology, clinical manifestations and diagnostic approaches, guideline-based treatment recommendations, drugs under development, and management challenges. EXPERT OPINION Future approaches to the management of NTM pulmonary disease will require therapies that are well tolerated, can be taken for a shorter time period and perhaps less frequently, have few drug-drug interactions, and are active against the various strains of pathogens. As the numbers of infections increase, such therapies will be welcomed by clinicians and patients.
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15
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Thapa J, Chizimu JY, Kitamura S, Akapelwa ML, Suwanthada P, Miura N, Toyting J, Nishimura T, Hasegawa N, Nishiuchi Y, Gordon SV, Nakajima C, Suzuki Y. Characterization of DNA Gyrase Activity and Elucidation of the Impact of Amino Acid Substitution in GyrA on Fluoroquinolone Resistance in Mycobacterium avium. Microbiol Spectr 2023; 11:e0508822. [PMID: 37067420 PMCID: PMC10269562 DOI: 10.1128/spectrum.05088-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/28/2023] [Indexed: 04/18/2023] Open
Abstract
Mycobacterium avium, a member of the M. avium complex (MAC), is the major pathogen contributing to nontuberculous mycobacteria (NTM) infections worldwide. Fluoroquinolones (FQs) are recommended for the treatment of macrolide-resistant MACs. The association of FQ resistance and mutations in the quinolone resistance-determining region (QRDR) of gyrA of M. avium is not yet clearly understood, as many FQ-resistant clinical M. avium isolates do not have such mutations. This study aimed to elucidate the role of amino acid substitution in the QRDR of M. avium GyrA in the development of FQ resistance. We found four clinical M. avium subsp. hominissuis isolates with Asp-to-Gly change at position 95 (Asp95Gly) and Asp95Tyr mutations in gyrA that were highly resistant to FQs and had 2- to 32-fold-higher MICs than the wild-type (WT) isolates. To clarify the contribution of amino acid substitutions to FQ resistance, we produced recombinant WT GyrA, GyrB, and four GyrA mutant proteins (Ala91Val, Asp95Ala, Asp95Gly, and Asp95Tyr) to elucidate their potential role in FQ resistance, using them to perform FQ-inhibited DNA supercoiling assays. While all the mutant GyrAs contributed to the higher (1.3- to 35.6-fold) FQ 50% inhibitory concentration (IC50) than the WT, Asp95Tyr was the most resistant mutant, with an IC50 15- to 35.6-higher than that of the WT, followed by the Asp95Gly mutant, with an IC50 12.5- to 17.6-fold higher than that of the WT, indicating that these amino acid substitutions significantly reduced the inhibitory activity of FQs. Our results showed that amino acid substitutions in the gyrA of M. avium contribute to FQ resistance. IMPORTANCE The emergence of fluoroquinolone (FQ) resistance has further compounded the control of emerging Mycobacterium avium-associated nontuberculous mycobacteria infections worldwide. For M. avium, the association of FQ resistance and mutations in the quinolone resistance-determining region (QRDR) of gyrA is not yet clearly understood. Here, we report that four clinical M. avium isolates with a mutation in the QRDR of gyrA were highly resistant to FQs. We further clarified the impact of mutations in the QRDR of GyrA proteins by performing in vitro FQ-inhibited DNA supercoiling assays. These results confirmed that, like in Mycobacterium tuberculosis, mutations in the QRDR of gyrA also strongly contribute to FQ resistance in M. avium. Since many FQ-resistant M. avium isolates do have these mutations, the detailed molecular mechanism of FQ resistance in M. avium needs further exploration.
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Affiliation(s)
- Jeewan Thapa
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Joseph Yamweka Chizimu
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Zambian National Public Health Institute, Ministry of Health, Lusaka, Zambia
| | - Soyoka Kitamura
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
| | - Mwangala Lonah Akapelwa
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Pondpan Suwanthada
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Nami Miura
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Jirachaya Toyting
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | - Naoki Hasegawa
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
- Office of Academic Research and Industry-Government Collaboration, Section of Microbial Genomics and Ecology, Hiroshima University, Higashi-Hiroshima, Japan
| | - Stephen V. Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Japan
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Liu Y, Moodley M, Pasipanodya JG, Gumbo T. Determining the Delamanid Pharmacokinetics/Pharmacodynamics Susceptibility Breakpoint Using Monte Carlo Experiments. Antimicrob Agents Chemother 2023; 67:e0140122. [PMID: 36877034 PMCID: PMC10112185 DOI: 10.1128/aac.01401-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 01/29/2023] [Indexed: 03/07/2023] Open
Abstract
Antimicrobial susceptibility testing, based on clinical breakpoints that incorporate pharmacokinetics/pharmacodynamics (PK/PD) and clinical outcomes, is becoming a new standard in guiding individual patient therapy as well as for drug resistance surveillance. However, for most antituberculosis drugs, breakpoints are instead defined by the epidemiological cutoff values of the MIC of phenotypically wild-type strains irrespective of PK/PD or dose. In this study, we determined the PK/PD breakpoint for delamanid by estimating the probability of target attainment for the approved dose administered at 100 mg twice daily using Monte Carlo experiments. We used the PK/PD targets (0- to 24-h area under the concentration-time curve to MIC) identified in a murine chronic tuberculosis model, hollow fiber system model of tuberculosis, early bactericidal activity studies of patients with drug-susceptible tuberculosis, and population pharmacokinetics in patients with tuberculosis. At the MIC of 0.016 mg/L, determined using Middlebrook 7H11 agar, the probability of target attainment was 100% in the 10,000 simulated subjects. The probability of target attainment fell to 25%, 40%, and 68% for PK/PD targets derived from the mouse model, the hollow fiber system model of tuberculosis, and patients, respectively, at the MIC of 0.031 mg/L. This indicates that an MIC of 0.016 mg/L is the delamanid PK/PD breakpoint for delamanid at 100 mg twice daily. Our study demonstrated that it is feasible to use PK/PD approaches to define a breakpoint for an antituberculosis drug.
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Affiliation(s)
- Yongge Liu
- Otsuka Pharmaceutical Development & Commercialization, Inc., Rockville, Maryland, USA
| | | | - Jotam G. Pasipanodya
- Quantitative Preclinical & Clinical Sciences Department, Praedicare Inc., Dallas, Texas, USA
| | - Tawanda Gumbo
- Quantitative Preclinical & Clinical Sciences Department, Praedicare Inc., Dallas, Texas, USA
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17
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Conformational space exploration of cryo-EM structures by variability refinement. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184133. [PMID: 36738875 DOI: 10.1016/j.bbamem.2023.184133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023]
Abstract
Cryo-EM observation of biological samples enables visualization of sample heterogeneity, in the form of discrete states that are separable, or continuous heterogeneity as a result of local protein motion before flash freezing. Variability analysis of this continuous heterogeneity describes the variance between a particle stack and a volume, and results in a map series describing the various steps undertaken by the sample in the particle stack. While this observation is absolutely stunning, it is very hard to pinpoint structural details to elements of the maps. In order to bridge the gap between observation and explanation, we designed a tool that refines an ensemble of structures into all the maps from variability analysis. Using this bundle of structures, it is easy to spot variable parts of the structure, as well as the parts that are not moving. Comparison with molecular dynamics simulations highlights the fact that the movements follow the same directions, albeit with different amplitudes. Ligand can also be investigated using this method. Variability refinement is available in the Phenix software suite, accessible under the program name phenix.varref.
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18
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Lorusso AB, Carrara JA, Barroso CDN, Tuon FF, Faoro H. Role of Efflux Pumps on Antimicrobial Resistance in Pseudomonas aeruginosa. Int J Mol Sci 2022; 23:15779. [PMID: 36555423 PMCID: PMC9779380 DOI: 10.3390/ijms232415779] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance is an old and silent pandemic. Resistant organisms emerge in parallel with new antibiotics, leading to a major global public health crisis over time. Antibiotic resistance may be due to different mechanisms and against different classes of drugs. These mechanisms are usually found in the same organism, giving rise to multidrug-resistant (MDR) and extensively drug-resistant (XDR) bacteria. One resistance mechanism that is closely associated with the emergence of MDR and XDR bacteria is the efflux of drugs since the same pump can transport different classes of drugs. In Gram-negative bacteria, efflux pumps are present in two configurations: a transmembrane protein anchored in the inner membrane and a complex formed by three proteins. The tripartite complex has a transmembrane protein present in the inner membrane, a periplasmic protein, and a porin associated with the outer membrane. In Pseudomonas aeruginosa, one of the main pathogens associated with respiratory tract infections, four main sets of efflux pumps have been associated with antibiotic resistance: MexAB-OprM, MexXY, MexCD-OprJ, and MexEF-OprN. In this review, the function, structure, and regulation of these efflux pumps in P. aeruginosa and their actions as resistance mechanisms are discussed. Finally, a brief discussion on the potential of efflux pumps in P. aeruginosa as a target for new drugs is presented.
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Affiliation(s)
- Andre Bittencourt Lorusso
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz, Curitiba 81350-010, Brazil
- School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba 80215-901, Brazil
| | - João Antônio Carrara
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz, Curitiba 81350-010, Brazil
| | | | - Felipe Francisco Tuon
- Laboratory of Emerging Infectious Diseases, Pontifícia Universidade Católica do Paraná, Curitiba 80215-901, Brazil
| | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz, Curitiba 81350-010, Brazil
- CHU de Quebec Research Center, Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec, QC G1V 0A6, Canada
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19
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Saeed DK, Ashraf J, Hasan Z, Shakoor S, Kanji A, Hasan R. Bedaquiline resistant Mycobacterium tuberculosis clinical isolates with and without rv0678 mutations have similar growth patterns under varying BDQ drug pressure. Tuberculosis (Edinb) 2022; 137:102266. [PMID: 36195000 DOI: 10.1016/j.tube.2022.102266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/18/2022] [Accepted: 09/23/2022] [Indexed: 01/24/2023]
Abstract
Resistance associated mutations have been reported to alter the growth of Mycobacterium tuberculosis (MTB) isolates under drug pressure. However, there is little information on the growth characteristics of bedaquiline (BDQ) resistant isolates in the presence of BDQ. To further understand the role of rv0678, we aimed to study whether the presence of rv0678 variants in BDQ resistant isolates alters the killing effect of BDQ. We, therefore, selected BDQ resistant clinical MTB isolates with (n = 6) and without (n = 3) variants in rv0678 gene. Using time kill assays, growth inhibition; taken as the relative change in log average colony forming unit (CFU)/ml at selected time points (24-96 h), was studied at Minimum Inhibitory Concentrations (MICs): 0x, 1x, 2.5x, 5x, 7.5x, 10x for these isolates. Growth inhibition was then analyzed using Kruskal Wallis and Kolmogorov Smirnov tests in PRISM vr.9. During the 24-96 h lag phase isolates with and without variants in rv0678 showed a similar growth inhibition pattern. No difference was noted in growth inhibition between BDQ resistant isolates and H37Rv. These findings suggest that role of alternate mechanisms in contributing to BDQ tolerance needs to be explored.
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Affiliation(s)
- Dania Khalid Saeed
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan.
| | - Javaria Ashraf
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan.
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan.
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan.
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan.
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan; Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, UK.
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20
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Barnabas V, Kashyap A, Raja R, Newar K, Rai D, Dixit NM, Mehra S. The Extent of Antimicrobial Resistance Due to Efflux Pump Regulation. ACS Infect Dis 2022; 8:2374-2388. [PMID: 36264222 DOI: 10.1021/acsinfecdis.2c00460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A key mechanism driving antimicrobial resistance (AMR) stems from the ability of bacteria to up-regulate efflux pumps upon exposure to drugs. The resistance gained by this up-regulation is pliable because of the tight regulation of efflux pump levels. This leads to temporary enhancement in survivability of bacteria due to higher efflux pump levels in the presence of antibiotics, which can be reversed when the cells are no longer exposed to the drug. Knowledge of the extent of resistance thus gained would inform intervention strategies aimed at mitigating AMR. Here, we combine mathematical modeling and experiments to quantify the maximum extent of resistance that efflux pump up-regulation can confer via phenotypic induction in the presence of drugs and genotypic abrogation of regulation. Our model describes the dynamics of drug transport in and out of cells coupled with the associated regulation of efflux pump levels and predicts the increase in the minimum inhibitory concentration (MIC) of drugs due to such regulation. To test the model, we measured the uptake and efflux as well as the MIC of the compound ethidium bromide (EtBr), a substrate of the efflux pump LfrA, in wild-type Mycobacterium smegmatis mc2155, as well as in two laboratory-generated strains. Our model captured the observed EtBr levels and MIC fold-changes quantitatively. Further, the model identified key parameters associated with the resulting resistance, variations in which could underlie the extent to which such resistance arises across different drug-bacteria combinations, potentially offering tunable handles to optimize interventions aimed at minimizing AMR.
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Affiliation(s)
- Vinay Barnabas
- Department of Chemical Engineering, Indian Institute of Technology, Mumbai400076, India
| | - Akanksha Kashyap
- Department of Chemical Engineering, Indian Institute of Technology, Mumbai400076, India
| | - Rubesh Raja
- Department of Chemical Engineering, Indian Institute of Science, Bangalore560012, India
| | - Kapil Newar
- Department of Chemical Engineering, Indian Institute of Science, Bangalore560012, India
| | - Deepika Rai
- Department of Chemical Engineering, Indian Institute of Technology, Mumbai400076, India
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore560012, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore560012, India
| | - Sarika Mehra
- Department of Chemical Engineering, Indian Institute of Technology, Mumbai400076, India
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21
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Patel S, Chapagain M, Mason C, Gingrich M, Athale S, Ribble W, Hoang T, Day J, Sun X, Jarvis T, Ochsner UA, Howe D, Gumbo T. Potency of the novel PolC DNA polymerase inhibitor CRS0540 in a disseminated Listeria monocytogenes intracellular hollow-fibre model. J Antimicrob Chemother 2022; 77:2876-2885. [PMID: 35929190 PMCID: PMC9525089 DOI: 10.1093/jac/dkac269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
Background Listeriosis is an orphan disease, which is nevertheless fatal in immunocompromised people. CRS0540 is a novel PolC DNA polymerase inhibitor that has demonstrated good in vitro and in vivo activity against Listeria monocytogenes. Methods Rodent-to-human allometry projection-based human population pharmacokinetics of CRS0540 were used for all studies. CRS0540 pharmacokinetics/pharmacodynamics studies in an intracellular hollow-fibre system model of disseminated listeriosis (HFS-Lister) examined the effect of eight treatment doses, administered daily over 7 days, in duplicate units. Total bacterial burden versus AUC/MIC exposures on each day were modelled using the inhibitory sigmoid Emax model, while CRS0540-resistant bacterial burden was modelled using a quadratic function. Ten thousand-subject Monte Carlo simulations were used to predict an optimal clinical dose for treatment. Results The mean CRS0540 intracellular/extracellular AUC0–24 ratio was 34.07 (standard error: 15.70) as measured in the HFS-Lister. CRS0540 demonstrated exposure-dependent bactericidal activity in the HFS-Lister, with the highest exposure killing approximately 5.0 log10 cfu/mL. The free drug AUC0–24/MIC associated with 80% of maximal kill (EC80) was 36.4. Resistance emergence versus AUC/MIC was described by a quadratic function, with resistance amplification at an AUC/MIC of 54.8 and resistance suppression at an AUC/MIC of 119. Monte Carlo simulations demonstrated that for the EC80 target, IV CRS0540 doses of 100 mg/kg achieved PTAs of >90% at MICs up to 1.0 mg/L. Conclusions CRS0540 is a promising orphan drug candidate for listeriosis. Future PK/PD studies comparing it with penicillin, the standard of care, could lead to this drug as a new treatment in immunocompromised patients.
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Affiliation(s)
- Swati Patel
- Hollow Fiber System & Experimental Therapeutics Laboratories, Praedicare Inc., Dallas, TX, USA
| | - Moti Chapagain
- Hollow Fiber System & Experimental Therapeutics Laboratories, Praedicare Inc., Dallas, TX, USA
| | | | | | - Shruti Athale
- Hollow Fiber System & Experimental Therapeutics Laboratories, Praedicare Inc., Dallas, TX, USA
| | | | | | | | | | | | | | - David Howe
- Hollow Fiber System & Experimental Therapeutics Laboratories, Praedicare Inc., Dallas, TX, USA.,Quantitative Preclinical & Clinical Sciences Department, Praedicare Inc., Dallas, TX, USA
| | - Tawanda Gumbo
- Hollow Fiber System & Experimental Therapeutics Laboratories, Praedicare Inc., Dallas, TX, USA.,Quantitative Preclinical & Clinical Sciences Department, Praedicare Inc., Dallas, TX, USA
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22
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López-Siles M, McConnell MJ, Martín-Galiano AJ. Identification of Promoter Region Markers Associated With Altered Expression of Resistance-Nodulation-Division Antibiotic Efflux Pumps in Acinetobacter baumannii. Front Microbiol 2022; 13:869208. [PMID: 35663863 PMCID: PMC9161033 DOI: 10.3389/fmicb.2022.869208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Genetic alterations leading to the constitutive upregulation of specific efflux pumps contribute to antibacterial resistance in multidrug resistant bacteria. The identification of such resistance markers remains one of the most challenging tasks of genome-level resistance predictors. In this study, 487 non-redundant genetic events were identified in upstream zones of three operons coding for resistance-nodulation-division (RND) efflux pumps of 4,130 Acinetobacter baumannii isolates. These events included insertion sequences, small indels, and single nucleotide polymorphisms. In some cases, alterations explicitly modified the expression motifs described for these operons, such as the promoter boxes, operators, and Shine-Dalgarno sequences. In addition, changes in DNA curvature and mRNA secondary structures, which are structural elements that regulate expression, were also calculated. According to their influence on RND upregulation, the catalog of upstream modifications were associated with “experimentally verified,” “presumed,” and “probably irrelevant” degrees of certainty. For experimental verification, DNA of upstream sequences independently carrying selected markers, three for each RND operon, were fused to a luciferase reporter plasmid system. Five out of the nine selected markers tested showed significant increases in expression with respect to the wild-type sequence control. In particular, a 25-fold expression increase was observed with the ISAba1 insertion sequence upstream the adeABC pump. Next, overexpression of each of the three multi-specific RND pumps was linked to their respective antibacterial substrates by a deep A. baumannii literature screen. Consequently, a data flow framework was then developed to link genomic upregulatory RND determinants to potential antibiotic resistance. Assignment of potential increases in minimal inhibitory concentrations at the “experimentally verified” level was permitted for 42 isolates to 7–8 unrelated antibacterial agents including tigecycline, which is overlooked by conventional resistome predictors. Thus, our protocol may represent a time-saving filter step prior to laborious confirmation experiments for efflux-driven resistance. Altogether, a computational-experimental pipeline containing all components required for identifying the upstream regulatory resistome is proposed. This schema may provide the foundational stone for the elaboration of tools approaching antibiotic efflux that complement routine resistome predictors for preventing antimicrobial therapy failure against difficult-to-threat bacteria.
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23
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Chapagain M, Pasipanodya JG, Athale S, Bernal C, Trammell R, Howe D, Gumbo T. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1694-1705. [PMID: 35257162 PMCID: PMC9155607 DOI: 10.1093/jac/dkac068] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/07/2022] [Indexed: 11/27/2022] Open
Abstract
Objectives The standard of care (SOC) for the treatment of pulmonary Mycobacterium avium complex (MAC) disease (clarithromycin, rifabutin, and ethambutol) achieves sustained sputum conversion rates of only 54%. Thus, new treatments should be prioritized. Methods We identified the omadacycline MIC against one laboratory MAC strain and calculated drug half life in solution, which we compared with measured MAC doubling times. Next, we performed an omadacycline hollow fibre system model of intracellular MAC (HFS-MAC) exposure–effect study, as well as the three-drug SOC, using pharmacokinetics achieved in patient lung lesions. Data was analysed using bacterial kill slopes (γ-slopes) and inhibitory sigmoid Emax bacterial burden versus exposure analyses. Monte Carlo experiments (MCE) were used to identify the optimal omadacycline clinical dose. Results Omadacycline concentration declined in solution with a half-life of 27.7 h versus a MAC doubling time of 16.3 h, leading to artefactually high MICs. Exposures mediating 80% of maximal effect changed up to 8-fold depending on sampling day with bacterial burden versus exposure analyses, while γ-slope-based analyses gave a single robust estimate. The highest omadacycline monotherapy γ-slope was −0.114 (95% CI: −0.141 to −0.087) (r2 = 0.98) versus −0.114 (95% CI: −0.133 to −0.094) (r2 = 0.99) with the SOC. MCEs demonstrated that 450 mg of omadacycline given orally on the first 2 days followed by 300 mg daily would achieve the AUC0-24 target of 39.67 mg·h/L. Conclusions Omadacycline may be a potential treatment option for pulmonary MAC, possibly as a back-bone treatment for a new MAC regimen and warrants future study in treatment of this disease.
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Affiliation(s)
- Moti Chapagain
- Hollow Fiber System & Experimental Therapeutics Laboratory, Praedicare Inc., 14830 Venture Drive, Dallas, Texas, USA
| | - Jotam G. Pasipanodya
- Quantitative Preclinical & Clinical Sciences Department, Praedicare Inc., 14830 Venture Drive, Dallas, Texas, USA
| | - Shruti Athale
- Hollow Fiber System & Experimental Therapeutics Laboratory, Praedicare Inc., 14830 Venture Drive, Dallas, Texas, USA
| | - Claude Bernal
- Praedicare Chemistry, Praedicare Inc., 14830 Venture Drive, Dallas, Texas, USA
| | - Rachel Trammell
- Praedicare Chemistry, Praedicare Inc., 14830 Venture Drive, Dallas, Texas, USA
| | - David Howe
- Hollow Fiber System & Experimental Therapeutics Laboratory, Praedicare Inc., 14830 Venture Drive, Dallas, Texas, USA
- Quantitative Preclinical & Clinical Sciences Department, Praedicare Inc., 14830 Venture Drive, Dallas, Texas, USA
- Praedicare Chemistry, Praedicare Inc., 14830 Venture Drive, Dallas, Texas, USA
| | - Tawanda Gumbo
- Hollow Fiber System & Experimental Therapeutics Laboratory, Praedicare Inc., 14830 Venture Drive, Dallas, Texas, USA
- Quantitative Preclinical & Clinical Sciences Department, Praedicare Inc., 14830 Venture Drive, Dallas, Texas, USA
- Corresponding author. E-mail:
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24
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Shome S, Sankar K, Jernigan RL. Simulated Drug Efflux for the AbgT Family of Membrane Transporters. J Chem Inf Model 2021; 61:5673-5681. [PMID: 34714659 DOI: 10.1021/acs.jcim.1c00516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Drug extrusion through molecular efflux pumps is an important mechanism for the survival of many pathogenic bacteria by removing drugs, providing multidrug resistance (MDR). Understanding molecular mechanisms for drug extrusion in multidrug efflux pumps is important for the development of new antiresistance drugs. The AbgT family of transporters involved in the folic acid biosynthesis pathway represents one such important efflux pump system. In addition to the transport of the folic acid precursor p-amino benzoic acid (PABA), members of this family are involved in the efflux of several sulfa drugs, conferring drug resistance to the bacteria. With the availability of structures for two members of this family (YdaH and MtrF), we investigate molecular pathways for transport of PABA and a sulfa drug (sulfamethazine) particularly for the YdaH transporter using steered molecular dynamics. Our analyses reveal the probable ligand migration pathways through the transporter, which also identifies key residues along the transport pathway. In addition, simulations using both PABA and sulfamethazine show how the protein is able to transport ligands of different shapes and sizes out of the pathogen. Our observations confirm previously reported functional residues for transport along the pathways by which YdaH transporters achieve antibiotic resistance to shuttle drugs out of the cells.
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Affiliation(s)
- Sayane Shome
- Bioinformatics and Computational Biology Program Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Kannan Sankar
- Bioinformatics and Computational Biology Program Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Robert L Jernigan
- Bioinformatics and Computational Biology Program Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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25
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Microbial Efflux Pump Inhibitors: A Journey around Quinoline and Indole Derivatives. Molecules 2021; 26:molecules26226996. [PMID: 34834098 PMCID: PMC8618814 DOI: 10.3390/molecules26226996] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/29/2022] Open
Abstract
Antimicrobial resistance (AMR) is a complex threat to human health and, to date, it represents a hot topic in drug discovery. The use of non-antibiotic molecules to block resistance mechanisms is a powerful alternative to the identification of new antibiotics. Bacterial efflux pumps exert the early step of AMR development, allowing the bacteria to grow in presence of sub-inhibitory drug concentration and develop more specific resistance mechanisms. Thus, efflux pump inhibitors (EPIs) offer a great opportunity to fight AMR, potentially restoring antibiotic activity. Based on our experience in designing and synthesizing novel EPIs, herein, we retrieved information around quinoline and indole derivatives reported in literature on this topic. Thus, our aim was to collect all data around these promising classes of EPIs in order to delineate a comprehensive structure–activity relationship (SAR) around each core for different microbes. With this review article, we aim to help future research in the field in the discovery of new microbial EPIs with improved activity and a better safety profile.
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26
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Flavonoids as Inhibitors of Bacterial Efflux Pumps. Molecules 2021; 26:molecules26226904. [PMID: 34833994 PMCID: PMC8625893 DOI: 10.3390/molecules26226904] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
Flavonoids are widely occurring secondary plant constituents, and are abundant in vegetable and fruit diets as well as herbal medicines. Therapeutic treatment options for bacterial infections are limited due to the spread of antimicrobial resistances. Hence, in a number of studies during the last few years, different classes of plant secondary metabolites as resistance-modifying agents have been carried out. In this review, we present the role of flavonoids as inhibitors of bacterial efflux pumps. Active compounds could be identified in the subclasses of chalcones, flavan-3-ols, flavanones, flavones, flavonols, flavonolignans and isoflavones; by far the majority of compounds were aglycones, although some glycosides like kaempferol glycosides with p-coumaroyl acylation showed remarkable results. Staphylococcus aureus NorA pump was the focus of many studies, followed by mycobacteria, whereas Gram-negative bacteria are still under-investigated.
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27
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The Mycobacterial Efflux Pump EfpA Can Induce High Drug Tolerance to Many Antituberculosis Drugs, Including Moxifloxacin, in Mycobacterium smegmatis. Antimicrob Agents Chemother 2021; 65:e0026221. [PMID: 34424047 DOI: 10.1128/aac.00262-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Active efflux of drugs across the membrane is a major survival strategy of bacteria against many drugs. In this work, we characterize an efflux pump, EfpA, from the major facilitator superfamily, that is highly conserved among both slow-growing and fast-growing Mycobacterium species and has been found to be upregulated in many clinical isolates of Mycobacterium tuberculosis. The gene encoding EfpA from Mycobacterium smegmatis was overexpressed under the control of both a constitutive and an inducible promoter. The expression of the efpA gene under the control of both promoters resulted in >32-fold-increased drug tolerance of M. smegmatis cells to many first-line (rifampicin, isoniazid, and streptomycin) and second-line (amikacin) antituberculosis drugs. Notably, the drug tolerance of M. smegmatis cells to moxifloxacin increased by more than 180-fold when efpA was overexpressed. The increase in MICs correlated with the decreased uptake of drugs, including norfloxacin, moxifloxacin, and ethidium bromide, and the high MIC could be reversed in the presence of an efflux pump inhibitor. A correlation was observed between the MICs of drugs and the efflux pump expression level, suggesting that the latter could be modulated by varying the expression level of the efflux pump. The expression of high levels of efpA did not impact the fitness of the cells when supplemented with glucose. The efpA gene is conserved across both pathogenic and nonpathogenic mycobacteria. The efpA gene from Mycobacterium bovis BCG/M. tuberculosis, which is 80% identical to efpA from M. smegmatis, also led to decreased antimicrobial efficacy of many drugs, although the fold change was lower. When overexpressed in M. bovis BCG, 8-fold-higher drug tolerance to moxifloxacin was observed. This is the first report of an efflux pump from Mycobacterium species that leads to higher drug tolerance to moxifloxacin, a promising new drug for the treatment of tuberculosis.
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28
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Ko DS, Kim NH, Kim EK, Ha EJ, Ro YH, Kim D, Choi KS, Kwon HJ. Comparative genomics of bovine mastitis-origin Staphylococcus aureus strains classified into prevalent human genotypes. Res Vet Sci 2021; 139:67-77. [PMID: 34256183 DOI: 10.1016/j.rvsc.2021.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 06/15/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Humans may serve as a reservoir host of Staphylococcus aureus, resulting in transmission to animals. Previously, we used RNA polymerase beta subunit gene (rpoB)-based genotyping and classified S. aureus strains into rpoB sequence types (RSTs). According to our previous work, the predominant genotypes of S. aureus in humans and cows differ in Korea, but some predominant genotypes (RST4-1 and RST2-1) in humans have been isolated from bovine mastitis. Therefore, it needs to be determined whether some strains of the predominant human genotypes have adapted to or caused occasional infections in cows. We determined the whole genome sequences of 2 bovine mastitis-origin strains, PMB179 (RST4-1) and PMB196 (RST2-1), and performed comparative genomics with the corresponding RST4-1 and RST2-1 S. aureus strains in the NCBI database. We identified 257 and 180 pseudogenes among 131 RST4-1 and 54 RST2-1 strains, respectively, for the comparison of pseudogene profiles. RST4-1 strains shared more common pseudogenes than RST2-1 strains, and some epidemiologically related strains shared common pseudogenes. However, most of the pseudogenes were strain-specific, and diverse pseudogene profiles were apparent in both the RST4-1 and RST2-1 strains. Furthermore, analysis of the mobile genetic elements, virulence genes, and antibiotic resistance genes revealed no molecular markers to differentiate PMB179 and PMB196 from human strains. Interestingly, the collective comparison of RST4-1 or RST2-1 strains revealed cumulative acquisition steps of genomic islands and antibiotic resistance genes. In conclusion, our data support PMB179 and PMB196 causing occasional infections that result in bovine mastitis.
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Affiliation(s)
- Dae-Sung Ko
- Laboratory of Poultry Medicine, Seoul National University, Seoul, Republic of Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Nam-Hyung Kim
- Laboratory of Poultry Medicine, Seoul National University, Seoul, Republic of Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Eun-Kyung Kim
- Department of Farm Animal Medicine, Seoul National University, Pyeongchang-gun, Republic of Korea
| | - Eun-Jin Ha
- Laboratory of Poultry Medicine, Seoul National University, Seoul, Republic of Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Young-Hye Ro
- Department of Farm Animal Medicine, Seoul National University, Pyeongchang-gun, Republic of Korea
| | - Danil Kim
- Department of Farm Animal Medicine, Seoul National University, Pyeongchang-gun, Republic of Korea
| | - Kang-Seuk Choi
- Laboratory of Avian Diseases, Seoul National University, Seoul, Republic of Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, Republic of Korea
| | - Hyuk-Joon Kwon
- Laboratory of Poultry Medicine, Seoul National University, Seoul, Republic of Korea; The Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul, Republic of Korea.
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29
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Mattoo R. Targeting emerging Mycobacterium avium infections: perspectives into pathways and antimicrobials for future interventions. Future Microbiol 2021; 16:753-764. [PMID: 34227394 DOI: 10.2217/fmb-2021-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium avium is an emerging opportunistic pathogen, globally. Infections caused by M. avium are laborious to treat and could result in drug resistance. This review discusses the importance of many factors including the cell wall in M. avium pathogenesis, since this unique structure modulates the pathogen's ability to thrive in various hosts and environmental niches including conferring resistance to killing by antimicrobials. More research efforts in future are solicited to develop novel therapeutics targeting M. avium. The complete eradication of M. avium infection in immunocompromised individuals would need a deeper understanding of the source of infection, unique underlying mechanisms and its uncharacterized pathways. This could, perhaps in future, hold the key to target and treat M. avium more effectively.
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Affiliation(s)
- Rohini Mattoo
- Divecha Centre for Climate Change, Indian Institute of Science, Bangalore, 560012, India
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30
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Genestet C, Hodille E, Barbry A, Berland JL, Hoffmann J, Westeel E, Bastian F, Guichardant M, Venner S, Lina G, Ginevra C, Ader F, Goutelle S, Dumitrescu O. Rifampicin exposure reveals within-host Mycobacterium tuberculosis diversity in patients with delayed culture conversion. PLoS Pathog 2021; 17:e1009643. [PMID: 34166469 PMCID: PMC8224949 DOI: 10.1371/journal.ppat.1009643] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/13/2021] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) genetic micro-diversity in clinical isolates may underline mycobacterial adaptation to tuberculosis (TB) infection and provide insights to anti-TB treatment response and emergence of resistance. Herein we followed within-host evolution of Mtb clinical isolates in two cohorts of TB patients, either with delayed Mtb culture conversion (> 2 months), or with fast culture conversion (< 2 months). We captured the genetic diversity of Mtb isolates obtained in each patient, by focusing on minor variants detected as unfixed single nucleotide polymorphisms (SNPs). To unmask antibiotic tolerant sub-populations, we exposed these isolates to rifampicin (RIF) prior to whole genome sequencing (WGS) analysis. Thanks to WGS, we detected at least 1 unfixed SNP within the Mtb isolates for 9/15 patients with delayed culture conversion, and non-synonymous (ns) SNPs for 8/15 patients. Furthermore, RIF exposure revealed 9 additional unfixed nsSNP from 6/15 isolates unlinked to drug resistance. By contrast, in the fast culture conversion cohort, RIF exposure only revealed 2 unfixed nsSNP from 2/20 patients. To better understand the dynamics of Mtb micro-diversity, we investigated the variant composition of a persistent Mtb clinical isolate before and after controlled stress experiments mimicking the course of TB disease. A minor variant, featuring a particular mycocerosates profile, became enriched during both RIF exposure and macrophage infection. The variant was associated with drug tolerance and intracellular persistence, consistent with the pharmacological modeling predicting increased risk of treatment failure. A thorough study of such variants not necessarily linked to canonical drug-resistance, but which are prone to promote anti-TB drug tolerance, may be crucial to prevent the subsequent emergence of resistance. Taken together, the present findings support the further exploration of Mtb micro-diversity as a promising tool to detect patients at risk of poorly responding to anti-TB treatment, ultimately allowing improved and personalized TB management. Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), bacteria that are able to persist inside the patient for many months or years, thus requiring long antibiotic treatments. Here we focused on TB patients with delayed response to treatment and we performed genetic characterization of Mtb isolates to search for sub-populations that may tolerate anti-TB drugs. We found that Mtb cultured from 9/15 patients contained different sub-populations, and in vitro drug exposure revealed Mtb sub-populations in 6/15 isolates, none related to known drug-resistance mechanisms. By contrast, drug exposure revealed Mtb sup-populations in 2/20 isolates in the control cohort of patients with fast culture conversion. Furthermore, we characterized a Mtb variant isolated from a sub-population growing in the presence of rifampicin (RIF), a major anti-TB drug. We found that this variant featured a modified lipidic envelope, and that it was able to develop in the presence of RIF and inside human macrophage cells. We performed pharmacological modelling and found that this kind of variant may be related to a poor response to treatment. In conclusion, searching for particular Mtb sub-populations may help to detect patients at risk of treatment failure and provide additional guidance for TB management.
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Affiliation(s)
- Charlotte Genestet
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- * E-mail:
| | - Elisabeth Hodille
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Alexia Barbry
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Jean-Luc Berland
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Jonathan Hoffmann
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Emilie Westeel
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Fabiola Bastian
- Plateforme DTAMB, CNRS, Université Lyon 1, Villeurbanne, France
| | - Michel Guichardant
- CarMeN laboratory, INSA Lyon, INSERM U1060, INRA U1397, Université Lyon 1, Villeurbanne, France
| | - Samuel Venner
- Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
| | - Gérard Lina
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
| | - Christophe Ginevra
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Florence Ader
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Service des Maladies infectieuses et tropicales, Lyon, France
| | - Sylvain Goutelle
- Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Service pharmaceutique, Lyon, France
| | - Oana Dumitrescu
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
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Sheikh BA, Bhat BA, Mehraj U, Mir W, Hamadani S, Mir MA. Development of New Therapeutics to Meet the Current Challenge of Drug Resistant Tuberculosis. Curr Pharm Biotechnol 2021; 22:480-500. [PMID: 32600226 DOI: 10.2174/1389201021666200628021702] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/01/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) is a prominent infective disease and a major reason of mortality/ morbidity globally. Mycobacterium tuberculosis causes a long-lasting latent infection in a significant proportion of human population. The increasing burden of tuberculosis is mainly caused due to multi drug-resistance. The failure of conventional treatment has been observed in large number of cases. Drugs that are used to treat extensively drug-resistant tuberculosis are expensive, have limited efficacy, and have more side effects for a longer duration of time and are often associated with poor prognosis. To regulate the emergence of multidrug resistant tuberculosis, extensively drug-resistant tuberculosis and totally drug resistant tuberculosis, efforts are being made to understand the genetic/molecular basis of target drug delivery and mechanisms of drug resistance. Understanding the molecular approaches and pathology of Mycobacterium tuberculosis through whole genome sequencing may further help in the improvement of new therapeutics to meet the current challenge of global health. Understanding cellular mechanisms that trigger resistance to Mycobacterium tuberculosis infection may expose immune associates of protection, which could be an important way for vaccine development, diagnostics, and novel host-directed therapeutic strategies. The recent development of new drugs and combinational therapies for drug-resistant tuberculosis through major collaboration between industry, donors, and academia gives an improved hope to overcome the challenges in tuberculosis treatment. In this review article, an attempt was made to highlight the new developments of drug resistance to the conventional drugs and the recent progress in the development of new therapeutics for the treatment of drugresistant and non-resistant cases.
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Affiliation(s)
- Bashir A Sheikh
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Basharat A Bhat
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Umar Mehraj
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Wajahat Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Suhail Hamadani
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
| | - Manzoor A Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar-190006, India
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Srivastava S, Chapagain M, van Zyl J, Deshpande D, Gumbo T. Potency of vancomycin against Mycobacterium tuberculosis in the hollow fiber system model. J Glob Antimicrob Resist 2021; 24:403-410. [PMID: 33508482 DOI: 10.1016/j.jgar.2021.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 12/11/2020] [Accepted: 01/05/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES To determine whether an inhaled vancomycin formulation resulting in high intrapulmonary 24-h area under the concentration-time curve (AUC0-24) could be optimised for tuberculosis treatment. We also explored vancomycin synergy and antagonism with d-cycloserine and benzylpenicillin. METHODS We determined MICs of two Mycobacterium tuberculosis (Mtb) laboratory strains (H37Ra and H37Rv) and two drug-susceptible and nine multidrug resistant clinical strains. Second, in the hollow fiber system model of TB [HFS-TB] using Mtb H37Ra strain, we recapitulated vancomycin intrapulmonary pharmacokinetics of eight doses administered twice daily over 28 days, mimicking a 6-h half-life. Using the HFS-TB, vancomycin was tested in combination with d-cycloserine and benzylpenicillin to determine synergy or antagonism between drugs targeting the same pathway. RESULTS Vancomycin MICs were 12 and 48 mg/L in drug-susceptible clinical isolates but >96 mg/L in all MDR isolates.In the HFS-TB, vancomycin killed 3.9 ± 0.6 log10 CFU/mL Mtb. The EC50 was calculated as AUC0-24/MIC of 184.6 ± 106.5. Compared with day 0, 1.0 and 2.0 log10 CFU/mL kill was achieved by AUC0-24/MIC of 168 and 685, respectively. Acquired vancomycin resistance developed to all vancomycin doses tested in the HFS-TB. In the HFS-TB, vancomycin was antagonistic to benzylpenicillin, which works downstream to glycopeptides in peptidoglycan synthesis, but synergistic with d-cycloserine, which inhibits upstream d-Ala-d-Ala ligase and alanine racemase. CONCLUSION Our proof-of-concept studies show that vancomycin optimal exposure target for Mtb kill could be achieved via inhalational drug delivery. Addition of drugs synergistic with vancomycin, e.g. d-cycloserine, may lower the vancomycin concentrations required to kill Mtb.
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Affiliation(s)
- Shashikant Srivastava
- Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, Tyler, TX, USA; Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Moti Chapagain
- Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, Tyler, TX, USA; Quantitative Preclinical and Clinical Sciences Department, Praedicare Inc., Dallas, TX, USA
| | - Johanna van Zyl
- Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Devyani Deshpande
- Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Tawanda Gumbo
- Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, Tyler, TX, USA; Quantitative Preclinical and Clinical Sciences Department, Praedicare Inc., Dallas, TX, USA; Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa.
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Bush NG, Diez-Santos I, Abbott LR, Maxwell A. Quinolones: Mechanism, Lethality and Their Contributions to Antibiotic Resistance. Molecules 2020; 25:E5662. [PMID: 33271787 PMCID: PMC7730664 DOI: 10.3390/molecules25235662] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 12/05/2022] Open
Abstract
Fluoroquinolones (FQs) are arguably among the most successful antibiotics of recent times. They have enjoyed over 30 years of clinical usage and become essential tools in the armoury of clinical treatments. FQs target the bacterial enzymes DNA gyrase and DNA topoisomerase IV, where they stabilise a covalent enzyme-DNA complex in which the DNA is cleaved in both strands. This leads to cell death and turns out to be a very effective way of killing bacteria. However, resistance to FQs is increasingly problematic, and alternative compounds are urgently needed. Here, we review the mechanisms of action of FQs and discuss the potential pathways leading to cell death. We also discuss quinolone resistance and how quinolone treatment can lead to resistance to non-quinolone antibiotics.
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Affiliation(s)
| | | | | | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; (N.G.B.); (I.D.-S.); (L.R.A.)
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Parker H, Lorenc R, Ruelas Castillo J, Karakousis PC. Mechanisms of Antibiotic Tolerance in Mycobacterium avium Complex: Lessons From Related Mycobacteria. Front Microbiol 2020; 11:573983. [PMID: 33101247 PMCID: PMC7554310 DOI: 10.3389/fmicb.2020.573983] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/01/2020] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium avium complex (MAC) species are the most commonly isolated nontuberculous mycobacteria to cause pulmonary infections worldwide. The lengthy and complicated therapy required to cure lung disease due to MAC is at least in part due to the phenomenon of antibiotic tolerance. In this review, we will define antibiotic tolerance and contrast it with persistence and antibiotic resistance. We will discuss physiologically relevant stress conditions that induce altered metabolism and antibiotic tolerance in mycobacteria. Next, we will review general molecular mechanisms underlying bacterial antibiotic tolerance, particularly those described for MAC and related mycobacteria, including Mycobacterium tuberculosis, with a focus on genes containing significant sequence homology in MAC. An improved understanding of antibiotic tolerance mechanisms can lay the foundation for novel approaches to target antibiotic-tolerant mycobacteria, with the goal of shortening the duration of curative treatment and improving survival in patients with MAC.
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Affiliation(s)
- Harley Parker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rachel Lorenc
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jennie Ruelas Castillo
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Petros C Karakousis
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
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Pereira AC, Ramos B, Reis AC, Cunha MV. Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches. Microorganisms 2020; 8:microorganisms8091380. [PMID: 32916931 PMCID: PMC7563442 DOI: 10.3390/microorganisms8091380] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 12/15/2022] Open
Abstract
Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.
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Affiliation(s)
- André C. Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Beatriz Ramos
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Ana C. Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Mónica V. Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal; (A.C.P.); (B.R.); (A.C.R.)
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal
- Correspondence: ; Tel.: +351-217-500-000 (ext. 22461)
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Wasserman S, Louw G, Ramangoaela L, Barber G, Hayes C, Omar SV, Maartens G, Barry C, Song T, Meintjes G. Linezolid resistance in patients with drug-resistant TB and treatment failure in South Africa. J Antimicrob Chemother 2020; 74:2377-2384. [PMID: 31081017 PMCID: PMC6640298 DOI: 10.1093/jac/dkz206] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 11/13/2022] Open
Abstract
Objectives Limited data exist on clinical associations and genotypic correlates of linezolid resistance in Mycobacterium tuberculosis. We aimed to describe mutations and clinical factors associated with phenotypic linezolid resistance from patients with drug-resistant TB at two public sector facilities in South Africa. Methods Adults and adolescents with treatment failure (culture positivity ≥4 months) on a linezolid-containing regimen were retrospectively identified. Phenotypic resistance, as defined by a linezolid MIC >1 mg/L, was assessed for retrieved isolates using broth microdilution. Targeted sequencing of rrl and rplC was performed, irrespective of growth on subculture. Results Thirty-nine patients with linezolid-based treatment failure were identified, 13 (33%) of whom had phenotypic or genotypic linezolid resistance after a median duration of 22 months (range = 7–32) of linezolid therapy. Paired MIC testing and genotyping was performed on 55 unique isolates. All isolates with phenotypic resistance (n = 16) were associated with known resistance mutations, most frequently due to the T460C substitution in rplC (n = 10); rrl mutations included G2814T, G2270C/T and A2810C. No mutations were detected in isolates with MICs at or below the critical concentration. Conclusions Linezolid resistance occurred in a third of patients with drug-resistant TB and treatment failure. Resistance occurred late and was predicted by a limited number of mutations in rrl and rplC. Screening for genotypic resistance should be considered for patients with a positive culture after 4 months of linezolid therapy in order to optimize treatment and avoid the toxicity of ineffective linezolid therapy.
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Affiliation(s)
- Sean Wasserman
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Gail Louw
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Limpho Ramangoaela
- Jose Pearson Hospital, Eastern Province Department of Health, Port Elizabeth, South Africa
| | - Garrick Barber
- Jose Pearson Hospital, Eastern Province Department of Health, Port Elizabeth, South Africa
| | - Cindy Hayes
- National Health Laboratory Service, TB Laboratory, Port Elizabeth, South Africa
| | - Shaheed Vally Omar
- Centre for Tuberculosis, WHO Supranational TB Reference Network, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Gary Maartens
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Clifton Barry
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Taeksun Song
- Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Graeme Meintjes
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Division of Infectious Diseases and HIV Medicine, Department of Medicine, University of Cape Town, Cape Town, South Africa
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Ruth MM, Magombedze G, Gumbo T, Bendet P, Sangen JJN, Zweijpfenning S, Hoefsloot W, Pennings L, Koeken VACM, Wertheim HFL, Lee PS, van Ingen J, Deshpande D. Minocycline treatment for pulmonary Mycobacterium avium complex disease based on pharmacokinetics/pharmacodynamics and Bayesian framework mathematical models. J Antimicrob Chemother 2020; 74:1952-1961. [PMID: 31039251 DOI: 10.1093/jac/dkz143] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 02/23/2019] [Accepted: 02/28/2019] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Our aim was to identify the pharmacokinetic/pharmacodynamic parameters of minocycline in the hollow-fibre system (HFS) model of pulmonary Mycobacterium avium complex (MAC) and to identify the optimal clinical dose. METHODS Minocycline MICs for 55 MAC clinical isolates from the Netherlands were determined. We also co-incubated primary isolated macrophages infected with MAC with minocycline. Next, we performed a 28 day HFS-MAC model dose-response study in which we mimicked pulmonary concentration-time profiles achieved in patients. The HFS-MAC model was sampled at intervals to determine the minocycline pharmacokinetics and MAC burden. We identified the AUC0-24/MIC ratios associated with 1.0 log10 cfu/mL kill below day 0 (stasis), defined as a bactericidal effect. We then performed 10000 Monte Carlo experiments to identify the optimal dose for a bactericidal effect in patients. RESULTS The MIC for 50% and 90% of cumulative clinical isolates was 8 and 64 mg/L, respectively. Minocycline decreased MAC bacterial burden below stasis in primary isolated macrophages. In the HFS-MAC model, minocycline achieved a microbial kill of 3.6 log10 cfu/mL below stasis. The AUC0-24/MIC exposure associated with a bactericidal effect was 59. Monte Carlo experiments identified a minocycline susceptibility MIC breakpoint of 16 mg/L. At this proposed breakpoint, the clinical dose of 200 mg/day achieved the bactericidal effect exposure target in ∼50% of patients, while 400 mg/day achieved this in 73.6% of patients, in Monte Carlo experiments. CONCLUSIONS Minocycline at a dose of 400 mg/day is expected to be bactericidal. We propose a clinical trial for validation.
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Affiliation(s)
- Mike M Ruth
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gesham Magombedze
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Paula Bendet
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Jasper J N Sangen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sanne Zweijpfenning
- Department of Pulmonary Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Wouter Hoefsloot
- Department of Pulmonary Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lian Pennings
- Department of Pulmonary Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Valerie A C M Koeken
- Radboud Center for Infectious Diseases, Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heiman F L Wertheim
- Department of Pulmonary Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pooi S Lee
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Devyani Deshpande
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
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Sibandze DB, Magazi BT, Malinga LA, Maningi NE, Shey BA, Pasipanodya JG, Mbelle NN. Machine learning reveals that Mycobacterium tuberculosis genotypes and anatomic disease site impacts drug resistance and disease transmission among patients with proven extra-pulmonary tuberculosis. BMC Infect Dis 2020; 20:556. [PMID: 32736602 PMCID: PMC7393820 DOI: 10.1186/s12879-020-05256-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 07/14/2020] [Indexed: 11/10/2022] Open
Abstract
Background There is a general dearth of information on extrapulmonary tuberculosis (EPTB). Here, we investigated Mycobacterium tuberculosis (Mtb) drug resistance and transmission patterns in EPTB patients treated in the Tshwane metropolitan area, in South Africa. Methods Consecutive Mtb culture-positive non-pulmonary samples from unique EPTB patients underwent mycobacterial genotyping and were assigned to phylogenetic lineages and transmission clusters based on spoligotypes. MTBDRplus assay was used to search mutations for isoniazid and rifampin resistance. Machine learning algorithms were used to identify clinically meaningful patterns in data. We computed odds ratio (OR), attributable risk (AR) and corresponding 95% confidence intervals (CI). Results Of the 70 isolates examined, the largest cluster comprised 25 (36%) Mtb strains that belonged to the East Asian lineage. East Asian lineage was significantly more likely to occur within chains of transmission when compared to the Euro-American and East-African Indian lineages: OR = 10.11 (95% CI: 1.56–116). Lymphadenitis, meningitis and cutaneous TB, were significantly more likely to be associated with drug resistance: OR = 12.69 (95% CI: 1.82–141.60) and AR = 0.25 (95% CI: 0.06–0.43) when compared with other EPTB sites, which suggests that poor rifampin penetration might be a contributing factor. Conclusions The majority of Mtb strains circulating in the Tshwane metropolis belongs to East Asian, Euro-American and East-African Indian lineages. Each of these are likely to be clustered, suggesting on-going EPTB transmission. Since 25% of the drug resistance was attributable to sanctuary EPTB sites notorious for poor rifampin penetration, we hypothesize that poor anti-tuberculosis drug dosing might have a role in the development of resistance.
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Affiliation(s)
- Doctor B Sibandze
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.,National Tuberculosis Control Program, Ministry of Health, Manzini, Kingdom of Eswatini
| | - Beki T Magazi
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.,Tshwane Division, National Health Laboratory Services, Pretoria, South Africa
| | - Lesibana A Malinga
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.,Tuberculosis Platform, South African Medical Research Council, Pretoria, South Africa
| | - Nontuthuko E Maningi
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa
| | - Bong-Akee Shey
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa
| | - Jotam G Pasipanodya
- Center For Infectious Diseases Research and Experimental Therapeutics, Texas Tech University Health Sciences Center, 5920 Forest Park Road, Dallas, TX, 75235, USA. .,Praedicare Laboratories, 14830 Venture Drive, Dallas, TX, 75234, USA.
| | - Nontombi N Mbelle
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Arcadia, Pretoria, 0007, South Africa.,Tshwane Division, National Health Laboratory Services, Pretoria, South Africa
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Thioridazine Is an Efflux Pump Inhibitor in Mycobacterium avium Complex but of Limited Clinical Relevance. Antimicrob Agents Chemother 2020; 64:AAC.00181-20. [PMID: 32312774 DOI: 10.1128/aac.00181-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/13/2020] [Indexed: 11/20/2022] Open
Abstract
Treatment of Mycobacterium avium complex pulmonary disease (MAC-PD) is challenging partly due to high efflux pump expression. Thioridazine might block these efflux pumps. We explore the efficacy of thioridazine against M. avium isolates using MICs, time-kill combination assays, ex vivo macrophage infection assays, and efflux assays. Thioridazine is bactericidal against M. avium, inhibits intracellular growth at 2× MIC, and blocks ethidium bromide efflux. However, its toxicity and low plasma concentrations make it unlikely to add efficacy to MAC-PD therapy.
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Rindi L. Efflux Pump Inhibitors Against Nontuberculous Mycobacteria. Int J Mol Sci 2020; 21:ijms21124191. [PMID: 32545436 PMCID: PMC7348771 DOI: 10.3390/ijms21124191] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 12/12/2022] Open
Abstract
Over the last years, nontuberculous mycobacteria (NTM) have emerged as important human pathogens. Infections caused by NTM are often difficult to treat due to an intrinsic multidrug resistance for the presence of a lipid-rich outer membrane, thus encouraging an urgent need for the development of new drugs for the treatment of mycobacterial infections. Efflux pumps (EPs) are important elements that are involved in drug resistance by preventing intracellular accumulation of antibiotics. A promising strategy to decrease drug resistance is the inhibition of EP activity by EP inhibitors (EPIs), compounds that are able to increase the intracellular concentration of antimicrobials. Recently, attention has been focused on identifying EPIs in mycobacteria that could be used in combination with drugs. The aim of the present review is to provide an overview of the current knowledge on EPs and EPIs in NTM and also, the effect of potential EPIs as well as their combined use with antimycobacterial drugs in various NTM species are described.
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Affiliation(s)
- Laura Rindi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, I-56127 Pisa, Italy
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Rodrigues L, Cravo P, Viveiros M. Efflux pump inhibitors as a promising adjunct therapy against drug resistant tuberculosis: a new strategy to revisit mycobacterial targets and repurpose old drugs. Expert Rev Anti Infect Ther 2020; 18:741-757. [PMID: 32434397 DOI: 10.1080/14787210.2020.1760845] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION In 2018, an estimated 377,000 people developed multidrug-resistant tuberculosis (MDR-TB), urging for new effective treatments. In the last years, it has been accepted that efflux pumps play an important role in the evolution of drug resistance. Strategies are required to mitigate the consequences of the activity of efflux pumps. AREAS COVERED Based upon the literature available in PubMed, up to February 2020, on the diversity of efflux pumps in Mycobacterium tuberculosis and their association with drug resistance, studies that identified efflux inhibitors and their effect on restoring the activity of antimicrobials subjected to efflux are reviewed. These support a new strategy for the development of anti-TB drugs, including efflux inhibitors, using in silico drug repurposing. EXPERT OPINION The current literature highlights the contribution of efflux pumps in drug resistance in M. tuberculosis and that efflux inhibitors may help to ensure the effectiveness of anti-TB drugs. However, despite the usefulness of efflux inhibitors in in vitro studies, in most cases their application in vivo is restricted due to toxicity. In a time when new drugs are needed to fight MDR-TB and extensively drug-resistant TB, cost-effective strategies to identify safer efflux inhibitors should be implemented in drug discovery programs.
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Affiliation(s)
- Liliana Rodrigues
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL , Lisboa, Portugal
| | - Pedro Cravo
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL , Lisboa, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL , Lisboa, Portugal
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Dobrzanska DA, Lamaudière MTF, Rollason J, Acton L, Duncan M, Compton S, Simms J, Weedall GD, Morozov IY. Preventive antibiotic treatment of calves: emergence of dysbiosis causing propagation of obese state-associated and mobile multidrug resistance-carrying bacteria. Microb Biotechnol 2020; 13:669-682. [PMID: 31663669 PMCID: PMC7111097 DOI: 10.1111/1751-7915.13496] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 08/27/2019] [Accepted: 10/01/2019] [Indexed: 01/10/2023] Open
Abstract
In agriculture, antibiotics are used for the treatment and prevention of livestock disease. Antibiotics perturb the bacterial gut composition but the extent of these changes and potential consequences for animal and human health is still debated. Six calves were housed in a controlled environment. Three animals received an injection of the antibiotic florfenicol (Nuflor), and three received no treatment. Faecal samples were collected at 0, 3 and 7 days, and bacterial communities were profiled to assess the impact of a therapy on the gut microbiota. Phylogenetic analysis (16S-rDNA) established that at day 7, antibiotic-treated microbiota showed a 10-fold increase in facultative anaerobic Escherichia spp, a signature of imbalanced microbiota, dysbiosis. The antibiotic resistome showed a high background of antibiotic resistance genes, which did not significantly change in response to florfenicol. However, the maintenance of Escherichia coli plasmid-encoded quinolone, oqxB and propagation of mcr-2, and colistin resistance genes were observed and confirmed by Sanger sequencing. The microbiota of treated animals was enriched with energy harvesting bacteria, common to obese microbial communities. We propose that antibiotic treatment of healthy animals leads to unbalanced, disease- and obese-related microbiota that promotes growth of E. coli carrying resistance genes on mobile elements, potentially increasing the risk of transmission of antibiotic resistant bacteria to humans.
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Affiliation(s)
| | | | | | - Lauren Acton
- School of Life SciencesCoventry UniversityCoventryUK
| | - Michael Duncan
- Centre for Sport, Exercise and Life SciencesCoventry UniversityCoventryUK
| | - Sharon Compton
- Moreton Morrell College FarmThe Warwickshire CollegeWarwickshireCV35 9BLUK
| | - John Simms
- School of Life SciencesCoventry UniversityCoventryUK
| | - Gareth D. Weedall
- School of Natural Sciences and PsychologyLiverpool John Moores UniversityLiverpoolUK
| | - Igor Y. Morozov
- Centre for Sport, Exercise and Life SciencesCoventry UniversityCoventryUK
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Feng Z, Liu D, Wang L, Wang Y, Zang Z, Liu Z, Song B, Gu L, Fan Z, Yang S, Chen J, Cui Y. A Putative Efflux Transporter of the ABC Family, YbhFSR, in Escherichia coli Functions in Tetracycline Efflux and Na +(Li +)/H + Transport. Front Microbiol 2020; 11:556. [PMID: 32390957 PMCID: PMC7190983 DOI: 10.3389/fmicb.2020.00556] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/16/2020] [Indexed: 12/20/2022] Open
Abstract
ATP-binding cassette transporters are ubiquitous in almost all organisms. The Escherichia coli genome is predicted to encode 69 ABC transporters. Eleven of the ABC transporters are presumed to be exporters, of which seven are possible drug export transporters. There has been minimal research on the function of YbhFSR, which is one of the putative drug resistance exporters. In this study, the ybhF gene of this transporter was characterized. Overexpression and knockout strains of ybhF were constructed. The ATPase activity of YbhF was studied using the malachite green assay, and the efflux abilities of knockout strains were demonstrated by using ethidium bromide (EB) as a substrate. The substrates of YbhFSR efflux, examined with the minimum inhibitory concentration (MIC), were determined to be tetracycline, oxytetracycline, chlortetracycline, doxycycline, EB, and Hoechst33342. Furthermore, tetracycline and EB efflux and accumulation experiments confirmed that the substrates of YbhFSR were tetracyclines and EB. The MIC assay and the fluorescence test results showed that tetracyclines are likely to be the major antibiotic substrate of YbhFSR. The existence of the signature NatA motif suggested that YbhFSR may also function as a Na+/H+ transporter. Overexpression of YbhF in E. coli KNabc lacking crucial Na+/H+ transporters conferred tolerance to NaCl, LiCl, and an alkaline pH. Together, the results showed that YbhFSR exhibited dual functions as a drug efflux pump and a Na+ (Li+)/H+ antiporter.
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Affiliation(s)
- Zhenyue Feng
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Defu Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Lizi Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yanhong Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhongjing Zang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhenhua Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Baifen Song
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Liwei Gu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Zhaowei Fan
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Siyu Yang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jing Chen
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Yudong Cui
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
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AlMatar M, Var I, Kayar B, Köksal F. Differential Expression of Resistant and Efflux Pump Genes in MDR-TB Isolates. Endocr Metab Immune Disord Drug Targets 2020; 20:271-287. [DOI: 10.2174/1871530319666191009153834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/21/2019] [Accepted: 07/22/2019] [Indexed: 12/20/2022]
Abstract
Background:Numerous investigations demonstrate efflux as a worldwide bacterial mode of action which contributes to the resistance of drugs. The activity of antibiotics, which subjects to efflux, can be improved by the combined usage of efflux inhibitors. However, the efflux role to the overall levels of antibiotic resistance of clinical M. tuberculosis isolates is inadequately comprehended and is still disregarded by many.Method:Here, we assessed the contribution of resistant genes associated with isoniazid (INH) and rifampin (R) resistance to the levels of drug resistance in the (27) clinical isolates of MDR-TB. Additionally, the role of the resistance for six putative drug efflux pump genes to the antibiotics was investigated. The level of katG expression was down-regulated in 24/27 (88.88%) of MDR-TB isolates. Of the 27 MDR-TB isolates, inhA, oxyR-ahpC, and rpoB showed either overexpression or up-regulation in 8 (29.62%), 4 (14.81 %), and 24 (88.88%), respectively. Moreover, the efflux pump genes drrA, drrB, efpA, Rv2459, Rv1634, and Rv1250 were overexpressed under INH/RIF plus fresh pomegranate juice (FPJ) stress signifying the efflux pumps contribution to the overall levels of the resistance of MDR-TB isolates.Conclusion:These results displayed that the levels of drug resistance of MDR-TB clinical isolates are due to combination among drug efflux pump and the presence of mutations in target genes, a truth which is often ignored by the specialists of tuberculosis in favour of the almost undoubted significance of drug target- gene mutations for the resistance in M. tuberculosis.
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Affiliation(s)
- Manaf AlMatar
- Department of Biotechnology, Institute of Natural and Applied Sciences (Fen Bilimleri Enstitusu), Cukurova University, Adana, Turkey
| | - Işıl Var
- Department of Food Engineering, Agricultural Faculty, Cukurova University, Adana, Turkey
| | - Begüm Kayar
- Department of Medical Microbiology, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Fatih Köksal
- Department of Medical Microbiology, Faculty of Medicine, Cukurova University, Adana, Turkey
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Guo Q, Chen J, Zhang S, Zou Y, Zhang Y, Huang D, Zhang Z, Li B, Chu H. Efflux Pumps Contribute to Intrinsic Clarithromycin Resistance in Clinical, Mycobacterium abscessus Isolates. Infect Drug Resist 2020; 13:447-454. [PMID: 32104016 PMCID: PMC7024787 DOI: 10.2147/idr.s239850] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 02/01/2020] [Indexed: 12/27/2022] Open
Abstract
Purpose The emergence of clarithromycin resistance is a challenge in treating Mycobacterium abscessus infections. Known mechanisms that contribute to intrinsic clarithromycin resistance focus on rrl gene-related mutations, but resistant clinical isolates often exhibit an inconsistent rrl genotype. Patients and Methods In this study, 194 clinical Mycobacterium abscessus isolates were collected from patients with lung infections and the whole genome of each isolate was sequenced. A comprehensive examination of the molecular mechanisms underlying intrinsic clarithromycin resistance was performed, combining MIC determination, comparative genome sequence analysis and qRT-PCR. Results Of the 194 isolates, 13 (6.7%) were clarithromycin resistant; only seven of these harbored a rrl 2270/2271 mutation. The remaining six resistant isolates did not exhibit a specific resistance-associated mutation in the clarithromycin target-site genes, rrl, rplC, rplD and rplV, or in the rrl modification gene erm(41). qRT-PCR analysis showed that the increased expression of the efflux pump genes, MAB_2355c, MAB_1409c and MAB_1846, as well as their positive regulatory gene whiB7, consistently correlated with increased clarithromycin resistance. The presence of efflux pump inhibitors significantly decreased the MIC of clarithromycin for nonsusceptible isolates, especially the intrinsic resistant isolates that exhibited no rrl 2270/2271 mutation. Conclusion These findings indicate that efflux pumps play a prominent role in the intrinsic resistance of M. abscessus to clarithromycin, complementing other known resistance mechanisms.
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Affiliation(s)
- Qi Guo
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China.,Tongji University School of Medicine, Shanghai 200092, People's Republic of China
| | - Jianhui Chen
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China.,Tongji University School of Medicine, Shanghai 200092, People's Republic of China
| | - Shaoyan Zhang
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
| | - Yuzhen Zou
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China.,Tongji University School of Medicine, Shanghai 200092, People's Republic of China
| | - Yongjie Zhang
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China.,Tongji University School of Medicine, Shanghai 200092, People's Republic of China
| | - Dongdong Huang
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
| | - Zhemin Zhang
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
| | - Bing Li
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
| | - Haiqing Chu
- Department of Respiratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China.,Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, People's Republic of China
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Deshpande D, Pasipanodya JG, Srivastava S, Bendet P, Koeuth T, Bhavnani SM, Ambrose PG, Smythe W, McIlleron H, Thwaites G, Gumusboga M, Van Deun A, Gumbo T. Gatifloxacin Pharmacokinetics/Pharmacodynamics-based Optimal Dosing for Pulmonary and Meningeal Multidrug-resistant Tuberculosis. Clin Infect Dis 2019; 67:S274-S283. [PMID: 30496459 DOI: 10.1093/cid/ciy618] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background Gatifloxacin is used for the treatment of multidrug-resistant tuberculosis (MDR-TB). The optimal dose is unknown. Methods We performed a 28-day gatifloxacin hollow-fiber system model of tuberculosis (HFS-TB) study in order to identify the target exposures associated with optimal kill rates and resistance suppression. Monte Carlo experiments (MCE) were used to identify the dose that would achieve the target exposure in 10000 adult patients with meningeal or pulmonary MDR-TB. The optimal doses identified were validated using probit analyses of clinical data from 2 prospective clinical trials of patients with pulmonary and meningeal tuberculosis. Classification and regression-tree (CART) analyses were used to identify the gatifloxacin minimum inhibitory concentration (MIC) below which patients failed or relapsed on combination therapy. Results The target exposure associated with optimal microbial kill rates and resistance suppression in the HFS-TB was a 0-24 hour area under the concentration-time curve-to-MIC of 184. MCE identified an optimal gatifloxacin dose of 800 mg/day for pulmonary and 1200 mg/day for meningeal MDR-TB, and a clinical susceptibility breakpoint of MIC ≤ 0.5 mg/L. In clinical trials, CART identified that 79% patients failed therapy if MIC was >2 mg/L, but 98% were cured if MIC was ≤0.5 mg/L. Probit analysis of clinical data demonstrated a >90% probability of a cure in patients if treated with 800 mg/day for pulmonary tuberculosis and 1200 mg/day for meningeal tuberculosis. Doses ≤400 mg/day were suboptimal. Conclusions Gatifloxacin doses of 800 mg/day and 1200 mg/day are recommended for pulmonary and meningeal MDR-TB treatment, respectively. Gatifloxacin has a susceptible dose-dependent zone at MICs 0.5-2 mg/L.
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Affiliation(s)
- Devyani Deshpande
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Jotam G Pasipanodya
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Shashikant Srivastava
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Paula Bendet
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Thearith Koeuth
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | | | - Paul G Ambrose
- Institute for Clinical Pharmacodynamics, Schenectady, New York
| | - Wynand Smythe
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory, South Africa
| | - Helen McIlleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Observatory, South Africa
| | - Guy Thwaites
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, Churchill Hospital, Oxford, United Kingdom.,Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Armand Van Deun
- Institute of Tropical Medicine, Antwerp, Belgium.,International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
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Multidrug ABC transporters in bacteria. Res Microbiol 2019; 170:381-391. [DOI: 10.1016/j.resmic.2019.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
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Effect of efflux pump inhibitors on the susceptibility of Mycobacterium avium complex to clarithromycin. J Antibiot (Tokyo) 2019; 73:128-132. [PMID: 31624335 DOI: 10.1038/s41429-019-0245-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 12/14/2022]
Abstract
In this study we aimed to evaluate the effect of the combination of clarithromycin and four inhibitors of efflux pumps (EPIs), including berberine (BER), carbonyl cyanide m-chlorophenylhydrazone (CCCP), piperine (PIP) and tetrandrine (TET), against 12 Mycobacterium avium complex clinical isolates. The minimum inhibitory concentration (MIC) of clarithromycin showed at least a fourfold reduction in presence of BER (83% of total isolates), CCCP (67%), PIP (25%) and TET (75%). Our results showed that the EPIs tested are active against both clarithromycin susceptible and resistant isolates. In particular, among the six resistant isolates, TET reversed the resistance phenotype of three strains, BER of two strains, and CCCP and PIP of one strain. Overall, our findings show the importance of these compounds in increasing the efficacy of clarithromycin in MAC clinical isolates.
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49
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Dheda K, Lenders L, Magombedze G, Srivastava S, Raj P, Arning E, Ashcraft P, Bottiglieri T, Wainwright H, Pennel T, Linegar A, Moodley L, Pooran A, Pasipanodya JG, Sirgel FA, van Helden PD, Wakeland E, Warren RM, Gumbo T. Drug-Penetration Gradients Associated with Acquired Drug Resistance in Patients with Tuberculosis. Am J Respir Crit Care Med 2019; 198:1208-1219. [PMID: 29877726 DOI: 10.1164/rccm.201711-2333oc] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Acquired resistance is an important driver of multidrug-resistant tuberculosis (TB), even with good treatment adherence. However, exactly what initiates the resistance and how it arises remain poorly understood. OBJECTIVES To identify the relationship between drug concentrations and drug susceptibility readouts (minimum inhibitory concentrations [MICs]) in the TB cavity. METHODS We recruited patients with medically incurable TB who were undergoing therapeutic lung resection while on treatment with a cocktail of second-line anti-TB drugs. On the day of surgery, antibiotic concentrations were measured in the blood and at seven prespecified biopsy sites within each cavity. Mycobacterium tuberculosis was grown from each biopsy site, MICs of each drug identified, and whole-genome sequencing performed. Spearman correlation coefficients between drug concentration and MIC were calculated. MEASUREMENTS AND MAIN RESULTS Fourteen patients treated for a median of 13 months (range, 5-31 mo) were recruited. MICs and drug resistance-associated single-nucleotide variants differed between the different geospatial locations within each cavity, and with pretreatment and serial sputum isolates, consistent with ongoing acquisition of resistance. However, pretreatment sputum MIC had an accuracy of only 49.48% in predicting cavitary MICs. There were large concentration-distance gradients for each antibiotic. The location-specific concentrations inversely correlated with MICs (P < 0.05) and therefore acquired resistance. Moreover, pharmacokinetic/pharmacodynamic exposures known to amplify drug-resistant subpopulations were encountered in all positions. CONCLUSIONS These data inform interventional strategies relevant to drug delivery, dosing, and diagnostics to prevent the development of acquired resistance. The role of high intracavitary penetration as a biomarker of antibiotic efficacy, when assessing new regimens, requires clarification.
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Affiliation(s)
- Keertan Dheda
- 1 Center for Lung Infection and Immunity, Division of Pulmonology and University of Cape Town Lung Institute, Department of Medicine.,2 Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Laura Lenders
- 1 Center for Lung Infection and Immunity, Division of Pulmonology and University of Cape Town Lung Institute, Department of Medicine
| | - Gesham Magombedze
- 3 Center for Infectious Diseases Research and Experimental Therapeutics and
| | | | - Prithvi Raj
- 4 Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Erland Arning
- 5 Institute of Metabolic Disease, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Paula Ashcraft
- 5 Institute of Metabolic Disease, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Teodoro Bottiglieri
- 5 Institute of Metabolic Disease, Baylor Research Institute, Baylor University Medical Center, Dallas, Texas
| | | | - Timothy Pennel
- 7 Chris Barnard Division of Cardiothoracic Surgery, Department of Surgery, Groote Schuur Hospital and University of Cape Town, Cape Town, South Africa
| | - Anthony Linegar
- 7 Chris Barnard Division of Cardiothoracic Surgery, Department of Surgery, Groote Schuur Hospital and University of Cape Town, Cape Town, South Africa
| | - Loven Moodley
- 7 Chris Barnard Division of Cardiothoracic Surgery, Department of Surgery, Groote Schuur Hospital and University of Cape Town, Cape Town, South Africa
| | - Anil Pooran
- 1 Center for Lung Infection and Immunity, Division of Pulmonology and University of Cape Town Lung Institute, Department of Medicine
| | | | - Frederick A Sirgel
- 8 Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research/Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Paul D van Helden
- 8 Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research/Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Edward Wakeland
- 4 Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Robin M Warren
- 8 Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research/Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa
| | - Tawanda Gumbo
- 1 Center for Lung Infection and Immunity, Division of Pulmonology and University of Cape Town Lung Institute, Department of Medicine.,3 Center for Infectious Diseases Research and Experimental Therapeutics and
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The Contribution of Efflux Pumps in Mycobacterium abscessus Complex Resistance to Clarithromycin. Antibiotics (Basel) 2019; 8:antibiotics8030153. [PMID: 31540480 PMCID: PMC6784190 DOI: 10.3390/antibiotics8030153] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 11/25/2022] Open
Abstract
The basis of drug resistance in Mycobacterium abscessus is still poorly understood. Nevertheless, as seen in other microorganisms, the efflux of antimicrobials may also play a role in M. abscessus drug resistance. Here, we investigated the role of efflux pumps in clarithromycin resistance using nine clinical isolates of M. abscessus complex belonging to the T28 erm(41) sequevar responsible for the inducible resistance to clarithromycin. The strains were characterized by drug susceptibility testing in the presence/absence of the efflux inhibitor verapamil and by genetic analysis of drug-resistance-associated genes. Efflux activity was quantified by real-time fluorometry. Efflux pump gene expression was studied by RT-qPCR upon exposure to clarithromycin. Verapamil increased the susceptibility to clarithromycin from 4- to ≥64-fold. The efflux pump genes MAB_3142 and MAB_1409 were found consistently overexpressed. The results obtained demonstrate that the T28 erm(41) polymorphism is not the sole cause of the inducible clarithromycin resistance in M.abscessus subsp. abscessus or bolletii with efflux activity providing a strong contribution to clarithromycin resistance. These data highlight the need for further studies on M. abscessus efflux response to antimicrobial stress in order to implement more effective therapeutic regimens and guidance in the development of new drugs against these bacteria.
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