1
|
Freiberg JA, Reyes Ruiz VM, Gimza BD, Murdoch CC, Green ER, Curry JM, Cassat JE, Skaar EP. Restriction of arginine induces antibiotic tolerance in Staphylococcus aureus. Nat Commun 2024; 15:6734. [PMID: 39112491 PMCID: PMC11306626 DOI: 10.1038/s41467-024-51144-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
Staphylococcus aureus is responsible for a substantial number of invasive infections globally each year. These infections are problematic because they are frequently recalcitrant to antibiotic treatment. Antibiotic tolerance, the ability of bacteria to persist despite normally lethal doses of antibiotics, contributes to antibiotic treatment failure in S. aureus infections. To understand how antibiotic tolerance is induced, S. aureus biofilms exposed to multiple anti-staphylococcal antibiotics are examined using both quantitative proteomics and transposon sequencing. These screens indicate that arginine metabolism is involved in antibiotic tolerance within a biofilm and support the hypothesis that depletion of arginine within S. aureus communities can induce antibiotic tolerance. Consistent with this hypothesis, inactivation of argH, the final gene in the arginine synthesis pathway, induces antibiotic tolerance. Arginine restriction induces antibiotic tolerance via inhibition of protein synthesis. In murine skin and bone infection models, an argH mutant has enhanced ability to survive antibiotic treatment with vancomycin, highlighting the relationship between arginine metabolism and antibiotic tolerance during S. aureus infection. Uncovering this link between arginine metabolism and antibiotic tolerance has the potential to open new therapeutic avenues targeting previously recalcitrant S. aureus infections.
Collapse
Affiliation(s)
- Jeffrey A Freiberg
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Valeria M Reyes Ruiz
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brittney D Gimza
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Caitlin C Murdoch
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Erin R Green
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Jacob M Curry
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James E Cassat
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Bone Biology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Eric P Skaar
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
| |
Collapse
|
2
|
Nyhoegen C, Bonhoeffer S, Uecker H. The many dimensions of combination therapy: How to combine antibiotics to limit resistance evolution. Evol Appl 2024; 17:e13764. [PMID: 39100751 PMCID: PMC11297101 DOI: 10.1111/eva.13764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 05/30/2024] [Accepted: 07/14/2024] [Indexed: 08/06/2024] Open
Abstract
In combination therapy, bacteria are challenged with two or more antibiotics simultaneously. Ideally, separate mutations are required to adapt to each of them, which is a priori expected to hinder the evolution of full resistance. Yet, the success of this strategy ultimately depends on how well the combination controls the growth of bacteria with and without resistance mutations. To design a combination treatment, we need to choose drugs and their doses and decide how many drugs get mixed. Which combinations are good? To answer this question, we set up a stochastic pharmacodynamic model and determine the probability to successfully eradicate a bacterial population. We consider bacteriostatic and two types of bactericidal drugs-those that kill independent of replication and those that kill during replication. To establish results for a null model, we consider non-interacting drugs and implement the two most common models for drug independence-Loewe additivity and Bliss independence. Our results show that combination therapy is almost always better in limiting the evolution of resistance than administering just one drug, even though we keep the total drug dose constant for a 'fair' comparison. Yet, exceptions exist for drugs with steep dose-response curves. Combining a bacteriostatic and a bactericidal drug which can kill non-replicating cells is particularly beneficial. Our results suggest that a 50:50 drug ratio-even if not always optimal-is usually a good and safe choice. Applying three or four drugs is beneficial for treatment of strains with large mutation rates but adding more drugs otherwise only provides a marginal benefit or even a disadvantage. By systematically addressing key elements of treatment design, our study provides a basis for future models which take further factors into account. It also highlights conceptual challenges with translating the traditional concepts of drug independence to the single-cell level.
Collapse
Affiliation(s)
- Christin Nyhoegen
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical BiologyMax Planck Institute for Evolutionary BiologyPlonGermany
| | - Sebastian Bonhoeffer
- Department of Environmental Systems Science, Institute of Integrative BiologyETH ZurichZurichSwitzerland
| | - Hildegard Uecker
- Research Group Stochastic Evolutionary Dynamics, Department of Theoretical BiologyMax Planck Institute for Evolutionary BiologyPlonGermany
| |
Collapse
|
3
|
Goss R, Adams VJ, Heinrich C, Grundon R, Linn-Pearl R, Scurrell E, Hamzianpour N. Progressive ulcerative keratitis in dogs in the United Kingdom: Microbial isolates, antimicrobial sensitivity, and resistance patterns. Vet Ophthalmol 2024; 27:330-346. [PMID: 37933885 DOI: 10.1111/vop.13160] [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: 06/17/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023]
Abstract
OBJECTIVES The objective of the study was to identify bacterial pathogens and their antimicrobial sensitivity profile associated with cases of canine progressive ulcerative keratitis. MATERIALS AND METHODS Analysis of microbial culture and sensitivity results from dogs with progressive ulcerative keratitis presenting to a UK referral practice between December 2018 and August 2020. RESULTS Positive bacterial cultures were obtained from 80/148 (54%) of the canine ulcers sampled with 99 bacterial isolates cultured. Streptococcus canis (n = 29), Pseudomonas aeruginosa (n = 19), and Staphylococcus pseudintermedius (n = 16) were the most common isolates. Pseudomonas aeruginosa was more likely to be isolated whether the ulcer was clinically malacic at the time of sampling (OR = 10.1, p < .001). Ulcers treated prior to culture with fusidic acid were 7.6 times more likely to be positive than those treated with any other antimicrobial(s). Bacterial isolates demonstrated resistance against neomycin (85%), fusidic acid (78%), and tetracycline (68%). Conversely, isolates were most likely to be sensitive to gentamicin (88%), ofloxacin (77%), ciprofloxacin (73%), and chloramphenicol (64%). Antimicrobial combinations of chloramphenicol or gentamicin with a fluoroquinolone (ofloxacin or ciprofloxacin) or chloramphenicol combined with gentamicin were the most effective on in vitro analysis (over 90% susceptibility of all isolates). CONCLUSION The most common bacterial species associated with canine progressive ulcerative keratitis in a UK referral population were S. canis, P. aeruginosa, and S. pseudintermedius. Combination antimicrobial therapy is recommended pending culture and sensitivity results given the varied antimicrobial susceptibility profiles and significant bacterial in vitro resistance to antimicrobial monotherapy.
Collapse
|
4
|
So JSP, Capule FR, Peña IG, Nacabuan SMJ, Ngo FLU, Robles YR, Ouano NNM, del Mar RR. Drug Utilization Review of Monitored Parenteral Antimicrobials in a Tertiary Care Private Hospital in Cebu City. ACTA MEDICA PHILIPPINA 2024; 58:35-48. [PMID: 38939423 PMCID: PMC11199354 DOI: 10.47895/amp.vi0.7249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Background Based on the 2017-2020 annual report of the Department of Health-Antimicrobial Resistance Surveillance Program, significant resistance patterns have been observed for common disease-causing pathogens. In the hospital setting, antimicrobial stewardship programs have been implemented to optimize the use of antimicrobials. Drug utilization review studies provide essential feedback to improve prescribing and use of medications. Objectives This study aimed to review drug utilization of monitored parenteral antimicrobials among patients admitted from January to December 2019. Methods The study employed a retrospective, cross-sectional, descriptive research design. A retrospective chart review of drugs administered to patients was conducted. Results A total of 821 patients charts met the inclusion criteria. The patients' ages ranged from 18 to 98 years old and 52% were females. General Internal Medicine practitioners (28%) were the top prescribers of monitored parenteral antimicrobials primarily for the management of moderate-risk community-acquired pneumonia (39%). They were mostly indicated for empirical treatment of infections (94%) and were given for an average of 5.73 days.Only 58% of the total cases had orders for culture and sensitivity testing. Of which, principally 47% had colony cultures. Blood (29%) and sputum (27%) were the most common specimens taken for culture and sensitivity testing. The microorganisms often isolated were Escherichia coli (19%), Klebsiella pneumoniae (18%), and Staphylococcus aureus (9%). In addition, extended-spectrum beta lactamase-producing gram-negative pathogens (4%) and methicillin-resistant S. aureus (1%) were also isolated. All the microorganisms isolated showed most resistance to ampicillin (81%) and most susceptibility to colistin (100%). There were drug therapy-related problems encountered. There was one case of an adverse drug reaction (0.1%) and two cases of contraindications (0.2%). Therapeutic duplication was also observed in 5% of the cases. Moreover, 39% had instances of drug-drug interactions.Piperacillin-tazobactam had the highest consumption (79.50 defined daily doses/1,000-patient days) among the monitored parenteral antimicrobials.Some prescriptions were deemed inappropriate upon evaluation. 12% of cases were inappropriate based on the justification indicator. As for the critical indicators, duration of therapy (78%) was the main reason. Only four components of the DUE criteria indicators have met or exceeded the established threshold level.The cost analysis indicated that the total actual cost of therapy with the monitored parenteral antimicrobials amounted to ₱17,645,601.73. Considering Department of Health National Antibiotic Guidelines recommendations, ideal total cost of treatment was ₱14,917,214.29. Potential cumulative cost savings of ₱2,728,387.44 could have been achieved for patients admitted last 2019. Conclusion Consumption of piperacillin-tazobactam was relatively high as compared to the other monitored parenteral antimicrobials covered in this study. Physicians at the study site seldom prescribe monitored parenteral antimicrobials as recommended by the National Antibiotic Guidelines. This is evidenced in the incidence of inappropriate therapy regimens, with inapt duration of therapy as the leading explanation.From the patient's perspective, the main economic implication was on the direct medical costs, particularly the increased cost of the actual antimicrobial therapy prescribed to manage various infections. Adherence of physicians to the established guidelines and selection of the most cost-effective therapy could have resulted in considerable cost savings.
Collapse
Affiliation(s)
- Jan Steven P. So
- Department of Pharmacy, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Francis R. Capule
- Department of Pharmacy, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Imelda G. Peña
- Department of Pharmacy, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Shiela May J. Nacabuan
- Department of Pharmacy, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Frances Lois U. Ngo
- Department of Pharmacy, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | - Yolanda R. Robles
- Department of Pharmacy, College of Pharmacy, University of the Philippines Manila, Manila, Philippines
| | | | - Ron R. del Mar
- AppleOne Medical Group, VisayasMed City Center, Cebu City, Cebu, Philippines
| |
Collapse
|
5
|
Chung CH, Chang DC, Rhoads NM, Shay MR, Srinivasan K, Okezue MA, Brunaugh AD, Chandrasekaran S. Transfer learning predicts species-specific drug interactions in emerging pathogens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597386. [PMID: 38895385 PMCID: PMC11185605 DOI: 10.1101/2024.06.04.597386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Machine learning (ML) algorithms are necessary to efficiently identify potent drug combinations within a large candidate space to combat drug resistance. However, existing ML approaches cannot be applied to emerging and under-studied pathogens with limited training data. To address this, we developed a transfer learning and crowdsourcing framework (TACTIC) to train ML models on data from multiple bacteria. TACTIC was built using 2,965 drug interactions from 12 bacterial strains and outperformed traditional ML models in predicting drug interaction outcomes for species that lack training data. Top TACTIC model features revealed genetic and metabolic factors that influence cross-species and species-specific drug interaction outcomes. Upon analyzing ~600,000 predicted drug interactions across 9 metabolic environments and 18 bacterial strains, we identified a small set of drug interactions that are selectively synergistic against Gram-negative (e.g., A. baumannii) and non-tuberculous mycobacteria (NTM) pathogens. We experimentally validated synergistic drug combinations containing clarithromycin, ampicillin, and mecillinam against M. abscessus, an emerging pathogen with growing levels of antibiotic resistance. Lastly, we leveraged TACTIC to propose selectively synergistic drug combinations to treat bacterial eye infections (endophthalmitis).
Collapse
Affiliation(s)
- Carolina H. Chung
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - David C. Chang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nicole M. Rhoads
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Madeline R. Shay
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Karthik Srinivasan
- Department of Ophthalmology and Visual Sciences, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Mercy A. Okezue
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, MI, 48109, USA
| | - Ashlee D. Brunaugh
- Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, Ann Arbor, MI, 48109, USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Bioinformatics and Computational Medicine, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| |
Collapse
|
6
|
Karlo J, Vijay A, Phaneeswar MS, Singh SP. Sensing the Bactericidal and Bacteriostatic Antimicrobial Mode of Action Using Raman Deuterium Stable Isotope Probing (DSIP) in Escherichia coli. ACS OMEGA 2024; 9:23753-23760. [PMID: 38854576 PMCID: PMC11154948 DOI: 10.1021/acsomega.4c01666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 06/11/2024]
Abstract
The mode of action of antibiotics can be broadly classified as bacteriostatic and bactericidal. The bacteriostatic mode leads to the arrested growth of the cells, while the bacteriocidal mode causes cell death. In this work, we report the applicability of deuterium stable isotope probing (DSIP) in combination with Raman spectroscopy (Raman DSIP) for discriminating the mode of action of antibiotics at the community level. Escherichia coli, a well-known model microbe, was used as an organism for the study. We optimized the concentration of deuterium oxide required for metabolic activity monitoring without compromising the microbial growth. Our findings suggest that changes in the intensity of the C-D band in the high-wavenumber region could serve as a quantifiable marker for determining the antibiotic mode of action. This can be used for early identification of the antibiotic's mode of action. Our results explore the new perspective that supports the utility of deuterium-based vibrational tags in the field of clinical spectroscopy. Understanding the antibiotic's mode of action on bacterial cells in a short and objective manner can significantly enhance the clinical management abilities of infectious diseases and may also help in personalized antimicrobial therapy.
Collapse
Affiliation(s)
- Jiro Karlo
- Department of Biosciences
and Bioengineering, Indian Institute of
Technology Dharwad, Dharwad, Karnataka 580011, India
| | - Arunsree Vijay
- Department of Biosciences
and Bioengineering, Indian Institute of
Technology Dharwad, Dharwad, Karnataka 580011, India
| | - Mahamkali Sri Phaneeswar
- Department of Biosciences
and Bioengineering, Indian Institute of
Technology Dharwad, Dharwad, Karnataka 580011, India
| | - Surya Pratap Singh
- Department of Biosciences
and Bioengineering, Indian Institute of
Technology Dharwad, Dharwad, Karnataka 580011, India
| |
Collapse
|
7
|
Gil-Gomez A, Rest JS. Wiring Between Close Nodes in Molecular Networks Evolves More Quickly Than Between Distant Nodes. Mol Biol Evol 2024; 41:msae098. [PMID: 38768245 PMCID: PMC11136681 DOI: 10.1093/molbev/msae098] [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: 12/21/2023] [Revised: 04/14/2024] [Accepted: 05/15/2024] [Indexed: 05/22/2024] Open
Abstract
As species diverge, a wide range of evolutionary processes lead to changes in protein-protein interaction (PPI) networks and metabolic networks. The rate at which molecular networks evolve is an important question in evolutionary biology. Previous empirical work has focused on interactomes from model organisms to calculate rewiring rates, but this is limited by the relatively small number of species and sparse nature of network data across species. We present a proxy for variation in network topology: variation in drug-drug interactions (DDIs), obtained by studying drug combinations (DCs) across taxa. Here, we propose the rate at which DDIs change across species as an estimate of the rate at which the underlying molecular network changes as species diverge. We computed the evolutionary rates of DDIs using previously published data from a high-throughput study in gram-negative bacteria. Using phylogenetic comparative methods, we found that DDIs diverge rapidly over short evolutionary time periods, but that divergence saturates over longer time periods. In parallel, we mapped drugs with known targets in PPI and cofunctional networks. We found that the targets of synergistic DDIs are closer in these networks than other types of DCs and that synergistic interactions have a higher evolutionary rate, meaning that nodes that are closer evolve at a faster rate. Future studies of network evolution may use DC data to gain larger-scale perspectives on the details of network evolution within and between species.
Collapse
Affiliation(s)
- Alejandro Gil-Gomez
- Department of Ecology and Evolution, Laufer Center for Physical and Quantitative Biology, Stony Brook University, 650 Life Sciences, Stony Brook, NY 11794-4254, USA
| | - Joshua S Rest
- Department of Ecology and Evolution, Laufer Center for Physical and Quantitative Biology, Stony Brook University, 650 Life Sciences, Stony Brook, NY 11794-4254, USA
| |
Collapse
|
8
|
Chowdhury R, Bhuia MS, Al Hasan MS, Ansari SA, Ansari IA, Gurgel APAD, Coutinho HDM, Islam MT. Anticonvulsant effect of (±) citronellal possibly through the GABAergic and voltage-gated sodium channel receptor interaction pathways: In vivo and in silico studies. Neurochem Int 2024; 175:105704. [PMID: 38395152 DOI: 10.1016/j.neuint.2024.105704] [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: 12/04/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 02/25/2024]
Abstract
This study aimed to investigate the anticonvulsant effects of citronellal (CIT) and possible underlying mechanisms through an isoniazid (INH)-induced seizure (convulsion) via in vivo and in silico studies. For this, convulsions were induced by the oral administration of INH (300 mg/kg) to the mice. The animals were treated orally with different doses of CIT (50, 100, and 200 mg/kg). Vehicle served as a negative control (NC), while diazepam (DZP) (2 mg/kg) and carbamazepine (CAR) (80 mg/kg) were provided (p.o.) as positive controls (PC). A combination therapy of CIT (middle dose) with DZP and CAR was also given to two separate groups of animals to estimate the synergistic or antagonistic effects. Molecular docking and visualization of ligand-receptor interactions are also estimated through different computational tools. The results of the in vivo study showed that CIT dose-dependently significantly (p < 0.05) exhibited a higher onset of seizures while reducing the frequency and duration of seizures in mice compared to the NC group. Besides these, in combination therapy, CIT significantly antagonized the activity of CAR and DZP, leading to a reduction in the onset of seizures and an increase in their frequency and duration compared to treatment with CAR and DZP alone. Additionally, molecular docking revealed that the CIT exhibited a moderate binding affinity (-5.8 kcal/mol) towards the GABAA receptor and a relative binding affinity (-5.3 kcal/mol) towards the voltage-gated sodium channel receptor by forming several bonds. In conclusion, CIT showed moderate anticonvulsant activity in INH-induced convulsion animals, possibly by enhancing GABAA receptor activity and inhibiting the voltage-gated sodium channel receptor.
Collapse
Affiliation(s)
- Raihan Chowdhury
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh
| | - Md Shimul Bhuia
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh; Bioluster Research Center, Gopalganj, 8100, Dhaka, Bangladesh
| | - Md Sakib Al Hasan
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh; Bioluster Research Center, Gopalganj, 8100, Dhaka, Bangladesh
| | - Siddique Akber Ansari
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Irfan Aamer Ansari
- Department of Drug Science and Technology, University of Turin, Turin, 10124, Italy
| | | | - Henrique Douglas Melo Coutinho
- Department of Biological Chemistry, Laboratory of Microbiology and Molecular Biology, Regional University of Cariri, Crato CE, 63105-000, Brazil CE, 63105-000, Brazil.
| | - Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh.
| |
Collapse
|
9
|
Batuman O, Britt-Ugartemendia K, Kunwar S, Yilmaz S, Fessler L, Redondo A, Chumachenko K, Chakravarty S, Wade T. The Use and Impact of Antibiotics in Plant Agriculture: A Review. PHYTOPATHOLOGY 2024; 114:885-909. [PMID: 38478738 DOI: 10.1094/phyto-10-23-0357-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Growers have depended on the specificity and efficacy of streptomycin and oxytetracycline as a part of their plant disease arsenal since the middle of the 20th century. With climate change intensifying plant bacterial epidemics, the established success of these antibiotics remains threatened. Our strong reliance on certain antibiotics for devastating diseases eventually gave way to resistance development. Although antibiotics in plant agriculture equal to less than 0.5% of overall antibiotic use in the United States, it is still imperative for humans to continue to monitor usage, environmental residues, and resistance in bacterial populations. This review provides an overview of the history and use, resistance and mitigation, regulation, environmental impact, and economics of antibiotics in plant agriculture. Bacterial issues, such as the ongoing Huanglongbing (citrus greening) epidemic in Florida citrus production, may need antibiotics for adequate control. Therefore, preserving the efficacy of our current antibiotics by utilizing more targeted application methods, such as trunk injection, should be a major focus. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Ozgur Batuman
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Kellee Britt-Ugartemendia
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Sanju Kunwar
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Salih Yilmaz
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Lauren Fessler
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Ana Redondo
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Kseniya Chumachenko
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | - Shourish Chakravarty
- Department of Food and Resource Economics, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Tara Wade
- Department of Food and Resource Economics, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| |
Collapse
|
10
|
Smith TP, Clegg T, Ransome E, Martin-Lilley T, Rosindell J, Woodward G, Pawar S, Bell T. High-throughput characterization of bacterial responses to complex mixtures of chemical pollutants. Nat Microbiol 2024; 9:938-948. [PMID: 38499812 PMCID: PMC10994839 DOI: 10.1038/s41564-024-01626-9] [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: 02/22/2023] [Accepted: 01/30/2024] [Indexed: 03/20/2024]
Abstract
Our understanding of how microbes respond to micropollutants, such as pesticides, is almost wholly based on single-species responses to individual chemicals. However, in natural environments, microbes experience multiple pollutants simultaneously. Here we perform a matrix of multi-stressor experiments by assaying the growth of model and non-model strains of bacteria in all 255 combinations of 8 chemical stressors (antibiotics, herbicides, fungicides and pesticides). We found that bacterial strains responded in different ways to stressor mixtures, which could not be predicted simply from their phylogenetic relatedness. Increasingly complex chemical mixtures were both more likely to negatively impact bacterial growth in monoculture and more likely to reveal net interactive effects. A mixed co-culture of strains proved more resilient to increasingly complex mixtures and revealed fewer interactions in the growth response. These results show predictability in microbial population responses to chemical stressors and could increase the utility of next-generation eco-toxicological assays.
Collapse
Affiliation(s)
- Thomas P Smith
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK.
| | - Tom Clegg
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Emma Ransome
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Thomas Martin-Lilley
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - James Rosindell
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Guy Woodward
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Samraat Pawar
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| | - Thomas Bell
- The Georgina Mace Centre for the Living Planet, Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, UK
| |
Collapse
|
11
|
Singh CP, Rai PK, Kumar M, Tiwari V, Tiwari A, Sharma A, Sharma K. Emphasis on Nanostructured Lipid Carriers in the Ocular Delivery of Antibiotics. Pharm Nanotechnol 2024; 12:126-142. [PMID: 37519002 DOI: 10.2174/2211738511666230727102213] [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: 03/22/2023] [Revised: 06/12/2023] [Accepted: 06/19/2023] [Indexed: 08/01/2023]
Abstract
BACKGROUND Drug distribution to the eye is still tricky because of the eye's intricate structure. Systemic delivery, as opposed to more traditional methods like eye drops and ointments, is more effective but higher doses can be harmful. OBJECTIVE The use of solid lipid nanoparticles (SLNPs) as a method of drug delivery has been the subject of research since the 1990s. Since SLNPs are derived from naturally occurring lipids, they pose no health risks to the user. To raise the eye's absorption of hydrophilic and lipophilic drugs, SLNs can promote corneal absorption and improve the ocular bioavailability of SLNPs. METHODS To address problems related to ocular drug delivery, many forms of nano formulation were developed. Some of the methods developed are, emulsification and ultra-sonication, high-speed stirring and ultra-sonication, thin layer hydration, adapted melt-emulsification, and ultrasonication techniques, hot o/w micro-emulsion techniques, etc. Results: Nanostructured lipid carriers are described in this review in terms of their ocular penetration mechanism, structural characteristic, manufacturing process, characterization, and advantages over other nanocarriers. CONCLUSION Recent developments in ocular formulations with nanostructured bases, such as surfacemodified attempts have been made to increase ocular bioavailability in both the anterior and posterior chambers by incorporating cationic chemicals into a wide variety of polymeric systems.
Collapse
Affiliation(s)
- Chandra Pratap Singh
- Usha college of Pharmacy & Medical Sciences, Vijaygaon, Ambedkar Nagar, 224122, UP, India
- Faculty of Pharmaceutical Sciences, Invertis University, Bareilly, 243123, UP, India
| | - Pankaj Kumar Rai
- Faculty of Pharmaceutical Sciences, Invertis University, Bareilly, 243123, UP, India
| | - Manish Kumar
- School of Pharmaceutical Sciences, CT University, Ludhiana, Punjab, India
| | - Varsha Tiwari
- Pharmacy Academy, IFTM University, Lodhipur-Rajput, Moradabad, 244102, India
| | - Abhishek Tiwari
- Pharmacy Academy, IFTM University, Lodhipur-Rajput, Moradabad, 244102, India
| | - Ajay Sharma
- School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, New Delhi, 110017, India
| | - Kamini Sharma
- School of Pharmaceutical Sciences, CT University, Ludhiana, Punjab, India
| |
Collapse
|
12
|
Bren A, Glass DS, Kohanim YK, Mayo A, Alon U. Tradeoffs in bacterial physiology determine the efficiency of antibiotic killing. Proc Natl Acad Sci U S A 2023; 120:e2312651120. [PMID: 38096408 PMCID: PMC10742385 DOI: 10.1073/pnas.2312651120] [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: 07/26/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023] Open
Abstract
Antibiotic effectiveness depends on a variety of factors. While many mechanistic details of antibiotic action are known, the connection between death rate and bacterial physiology is poorly understood. A common observation is that death rate in antibiotics rises linearly with growth rate; however, it remains unclear how other factors, such as environmental conditions and whole-cell physiological properties, affect bactericidal activity. To address this, we developed a high-throughput assay to precisely measure antibiotic-mediated death. We found that death rate is linear in growth rate, but the slope depends on environmental conditions. Growth under stress lowers death rate compared to nonstressed environments with similar growth rate. To understand stress's role, we developed a mathematical model of bacterial death based on resource allocation that includes a stress-response sector; we identify this sector using RNA-seq. Our model accurately predicts the minimal inhibitory concentration (MIC) with zero free parameters across a wide range of growth conditions. The model also quantitatively predicts death and MIC when sectors are experimentally modulated using cyclic adenosine monophosphate (cAMP), including protection from death at very low cAMP levels. The present study shows that different conditions with equal growth rate can have different death rates and establishes a quantitative relation between growth, death, and MIC that suggests approaches to improve antibiotic efficacy.
Collapse
Affiliation(s)
- Anat Bren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - David S. Glass
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Yael Korem Kohanim
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT06520
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot7610001, Israel
| |
Collapse
|
13
|
Dunster E, Johnson WL, Wozniak RAF. Antimicrobial Drug-Drug Interactions in the Treatment of Infectious Keratitis. Cornea 2023; 42:1555-1561. [PMID: 37106486 PMCID: PMC10611897 DOI: 10.1097/ico.0000000000003304] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023]
Abstract
PURPOSE Infectious keratitis is a serious disease requiring immediate, intensive, and broad-spectrum empiric treatment to prevent vision loss. Given the diversity of organisms that can cause serious corneal disease, current guidelines recommend treatment with several antimicrobial agents simultaneously to provide adequate coverage while awaiting results of microbiology cultures. However, it is currently unknown how the use of multiple ophthalmic antimicrobial agents in combination may affect the efficacy of individual drugs. METHODS Using a panel of 9 ophthalmic antibiotics, 3 antifungal agents, and 2 antiacanthamoeba therapeutics, fractional inhibitory concentration testing in the standard checkerboard format was used to study 36 antibiotic-antibiotic combinations, 27 antibiotic-antifungal combinations, and 18 antibiotic-antiacanthamoeba combinations against both Staphylococcus aureus and Pseudomonas aeruginosa for synergistic, additive, neutral, or antagonistic drug-drug interactions. RESULTS We demonstrate that while most combinations resulted in no change in antimicrobial efficacy of individual components, the combination of erythromycin + polyhexamethylene biguanide was found to be antagonistic toward P. aeruginosa . Conversely, 18 combinations toward S. aureus and 15 combinations toward P. aeruginosa resulted in additive or synergistic activity, including 4 with improved activity toward both species. CONCLUSIONS Understanding how drug-drug interactions may affect drug efficacy is critical to selecting the appropriate combination therapy and improving clinical outcomes of this blinding disease.
Collapse
Affiliation(s)
- Elianna Dunster
- Department of Ophthalmology, University of Rochester School of Medicine and Dentistry, Rochester, NY
| | | | | |
Collapse
|
14
|
Chowdhury F, Findlay BL. Fitness Costs of Antibiotic Resistance Impede the Evolution of Resistance to Other Antibiotics. ACS Infect Dis 2023; 9:1834-1845. [PMID: 37726252 PMCID: PMC10581211 DOI: 10.1021/acsinfecdis.3c00156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Indexed: 09/21/2023]
Abstract
Antibiotic resistance is a major threat to global health, claiming the lives of millions every year. With a nearly dry antibiotic development pipeline, novel strategies are urgently needed to combat resistant pathogens. One emerging strategy is the use of sequential antibiotic therapy, postulated to reduce the rate at which antibiotic resistance evolves. Here, we use the soft agar gradient evolution (SAGE) system to carry out high-throughput in vitro bacterial evolution against antibiotic pressure. We find that evolution of resistance to the antibiotic chloramphenicol (CHL) severely affects bacterial fitness, slowing the rate at which resistance to the antibiotics nitrofurantoin and streptomycin emerges. In vitro acquisition of compensatory mutations in the CHL-resistant cells markedly improves fitness and nitrofurantoin adaptation rates but fails to restore rates to wild-type levels against streptomycin. Genome sequencing reveals distinct evolutionary paths to resistance in fitness-impaired populations, suggesting resistance trade-offs in favor of mitigation of fitness costs. We show that the speed of bacterial fronts in SAGE plates is a reliable indicator of adaptation rates and evolutionary trajectories to resistance. Identification of antibiotics whose mutational resistance mechanisms confer stable impairments may help clinicians prescribe sequential antibiotic therapies that are less prone to resistance evolution.
Collapse
Affiliation(s)
- Farhan
R. Chowdhury
- Department
of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Brandon L. Findlay
- Department
of Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Department
of Chemistry and Biochemistry, Concordia
University, Montréal, Québec H4B 1R6, Canada
| |
Collapse
|
15
|
Wood E, Schulenburg H, Rosenstiel P, Bergmiller T, Ankrett D, Gudelj I, Beardmore R. Ribosome-binding antibiotics increase bacterial longevity and growth efficiency. Proc Natl Acad Sci U S A 2023; 120:e2221507120. [PMID: 37751555 PMCID: PMC10556576 DOI: 10.1073/pnas.2221507120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 07/11/2023] [Indexed: 09/28/2023] Open
Abstract
Antibiotics, by definition, reduce bacterial growth rates in optimal culture conditions; however, the real-world environments bacteria inhabit see rapid growth punctuated by periods of low nutrient availability. How antibiotics mediate population decline during these periods is poorly understood. Bacteria cannot optimize for all environmental conditions because a growth-longevity tradeoff predicts faster growth results in faster population decline, and since bacteriostatic antibiotics slow growth, they should also mediate longevity. We quantify how antibiotics, their targets, and resistance mechanisms influence longevity using populations of Escherichia coli and, as the tradeoff predicts, populations are maintained for longer if they encounter ribosome-binding antibiotics doxycycline and erythromycin, a finding that is not observed using antibiotics with alternative cellular targets. This tradeoff also predicts resistance mechanisms that increase growth rates during antibiotic treatment could be detrimental during nutrient stresses, and indeed, we find resistance by ribosomal protection removes benefits to longevity provided by doxycycline. We therefore liken ribosomal protection to a "Trojan horse" because it provides protection from an antibiotic but, during nutrient stresses, it promotes the demise of the bacteria. Seeking mechanisms to support these observations, we show doxycycline promotes efficient metabolism and reduces the concentration of reactive oxygen species. Seeking generality, we sought another mechanism that affects longevity and we found the number of doxycycline targets, namely, the ribosomal RNA operons, mediates growth and longevity even without antibiotics. We conclude that slow growth, as observed during antibiotic treatment, can help bacteria overcome later periods of nutrient stress.
Collapse
Affiliation(s)
- Emily Wood
- Biosciences, College of Life and Environmental Sciences, University of Exeter, ExeterEX4 4QD, United Kingdom
- Engineering and Physical Sciences Research Council Hub for Quantitative Modelling in Healthcare, University of Exeter, ExeterEX4 4QJ, United Kingdom
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoologisches Institut, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, Kiel24118, Germany
| | - Philip Rosenstiel
- Instituts für Klinische Molekularbiologie, Dekanat der Medizinischen Fakultät, Christian-Albrechts-Universität zu Kiel, Christian-Albrechts-Platz 4, KielD-24118, Germany
| | - Tobias Bergmiller
- Biosciences, College of Life and Environmental Sciences, University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Dyan Ankrett
- Biosciences, College of Life and Environmental Sciences, University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Ivana Gudelj
- Biosciences, College of Life and Environmental Sciences, University of Exeter, ExeterEX4 4QD, United Kingdom
| | - Robert Beardmore
- Biosciences, College of Life and Environmental Sciences, University of Exeter, ExeterEX4 4QD, United Kingdom
- Engineering and Physical Sciences Research Council Hub for Quantitative Modelling in Healthcare, University of Exeter, ExeterEX4 4QJ, United Kingdom
| |
Collapse
|
16
|
Lee WW, Seo JW, Jang IS, Kwon YJ, Joung WJ, Jun JH, Kim J, Son D, Lim SW, Yun SH, Tallarico M, Park CJ. Comparison of Prophylactic Effects between Localized Biomimetic Minocycline and Systematic Amoxicillin on Implants Placed Immediately in Infected Sockets. Biomimetics (Basel) 2023; 8:461. [PMID: 37887592 PMCID: PMC10604678 DOI: 10.3390/biomimetics8060461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 10/28/2023] Open
Abstract
This study evaluated the prophylactic effect of localized biomimetic minocycline and systemic amoxicillin on immediate implant placement at infected extraction sites. Twelve mongrels with six implants each were randomly assigned to five groups: uninfected negative control (Group N); infected with oral complex bacteria (Group P); infected and treated with amoxicillin one hour before implant placement (Group A); infected and treated with minocycline during implant placement (Group B); and infected and treated with amoxicillin one hour before implant placement and with minocycline during implant placement (Group C). Radiographic bone level, gingival index (GI), probing depth (PD), papillary bleeding index (PBI), and removal torque (RT) were recorded. There was no significant difference between Groups A, B, and C for bone loss. Group A showed the highest RT, the lowest PBI, and significantly lower GI and PD values than Group P. Group B exhibited significantly higher RT value than Group N and significantly smaller PD value than Group P at 6 w postoperatively. Localized minocycline could improve implant success by reducing bone loss and increasing RT and systemic amoxicillin could maintain the stability of the peri-implant soft tissue. However, combined use of these two antibiotics did not augment the prophylactic effect.
Collapse
Affiliation(s)
- Won-Woo Lee
- Division of Oral & Maxillofacial Surgery, Department of Dentistry, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Jin-Won Seo
- Division of Oral & Maxillofacial Surgery, Department of Dentistry, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Il-Seok Jang
- Osstem R&D Center, Seoul 07789, Republic of Korea
| | | | - Won-Jun Joung
- Division of Oral & Maxillofacial Surgery, Department of Dentistry, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Jong-Hun Jun
- Division of Oral & Maxillofacial Surgery, Department of Dentistry, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Jiyeong Kim
- Department of Pre-Medicine, College of Medicine and Biostatistics Lab, Medical Research Collaborating Center (MRCC), Hanyang University, Seoul 04763, Republic of Korea
| | - Donghee Son
- Laboratory of Biostatistical Consulting and Research, Medical Research Collaborating Center, Industry-University Cooperation Foundation, Hanyang University, Seoul 04763, Republic of Korea
| | - Seung-Weon Lim
- Division of Orthodontics, Department of Dentistry, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Seo-Hyoung Yun
- Division of Oral & Maxillofacial Surgery, Department of Dentistry, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| | - Marco Tallarico
- Department of Medicine, Surgery, and Pharmacy, University of Sassari, 07021 Sassari, Italy
| | - Chang-Joo Park
- Division of Oral & Maxillofacial Surgery, Department of Dentistry, College of Medicine, Hanyang University, Seoul 04763, Republic of Korea
| |
Collapse
|
17
|
Lv J, Liu G, Ju Y, Huang H, Li D, Sun Y. Identification of Robust Antibiotic Subgroups by Integrating Multi-Species Drug-Drug Interactions. J Chem Inf Model 2023; 63:4970-4978. [PMID: 37459588 DOI: 10.1021/acs.jcim.3c00937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Previous studies have shown that antibiotics can be divided into groups, and drug-drug interactions (DDI) depend on their groups. However, these studies focused on a specific bacteria strain (i.e., Escherichia coli BW25113). Existing datasets often contain noise. Noisy labeled data may have a bad effect on the clustering results. To address this problem, we developed a multi-source information fusion method for integrating DDI information from multiple bacterial strains. Specifically, we calculated drug similarities based on the DDI network of each bacterial strain and then fused these drug similarity matrices to obtain a new fused similarity matrix. The fused similarity matrix was combined with the T-distributed stochastic neighbor embedding algorithm, and hierarchical clustering algorithm can effectively identify antibiotic subgroups. These antibiotic subgroups are strongly correlated with known antibiotic classifications, and group-group interactions are almost monochromatic. In summary, our method provides a promising framework for understanding the mechanism of action of antibiotics and exploring multi-species group-group interactions.
Collapse
Affiliation(s)
- Ji Lv
- College of Computer Science and Technology, Jilin University, Changchun 130000, China
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130000, China
| | - Guixia Liu
- College of Computer Science and Technology, Jilin University, Changchun 130000, China
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130000, China
| | - Yuan Ju
- Sichuan University Library, Sichuan University, 610000 Chengdu, China
| | - Houhou Huang
- College of Chemistry, Jilin University, Changchun 130000, China
| | - Dalin Li
- School of Computer Science, Zhuhai College of Science and Technology, Zhuhai 519041, China
| | - Ying Sun
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun 130000, China
| |
Collapse
|
18
|
Lv J, Liu G, Ju Y, Sun B, Huang H, Sun Y. Integrating multi-source drug information to cluster drug-drug interaction network. Comput Biol Med 2023; 162:107088. [PMID: 37263154 DOI: 10.1016/j.compbiomed.2023.107088] [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: 03/16/2023] [Revised: 05/10/2023] [Accepted: 05/27/2023] [Indexed: 06/03/2023]
Abstract
Characterizing drug-drug interactions is important to improve efficacy and/or slow down the evolution of antimicrobial resistance. Experimental methods are both time-consuming and laborious for characterizing drug-drug interactions. In recent years, many computational methods have been proposed to explore drug-drug interactions. However, these methods failed to effectively integrate multi-source drug information. In this study, we propose a similarity matrix fusion (SMF) method to integrate four drug information (i.e., structural similarity, pharmaceutical similarity, phenotypic similarity and therapeutic similarity). SMF combined with t-distributed stochastic neighbor embedding (t-SNE) and hierarchical clustering algorithm can effectively identify drug groups and group-group interactions are almost monochromatic (purely synergetic or purely antagonistic). To evaluate clustering quality (i.e., monochromaticity), two measures (edge purity and edge normalized mutual information) are proposed, and SMF showed the best performance. In addition, clustered drug-drug interaction network can also be used to predict new drug-drug interactions (accuracy = 0.741). Overall, SMF provides a comprehensive view to understand drug groups and group-group interactions.
Collapse
Affiliation(s)
- Ji Lv
- College of Computer Science and Technology, Jilin University, Changchun, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Guixia Liu
- College of Computer Science and Technology, Jilin University, Changchun, China; Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China.
| | - Yuan Ju
- Sichuan University Library, Sichuan University, Chengdu, China
| | - Binwen Sun
- Second Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Houhou Huang
- College of Chemistry, Jilin University, Changchun, China
| | - Ying Sun
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, China
| |
Collapse
|
19
|
Doganay MT, Chelliah CJ, Tozluyurt A, Hujer AM, Obaro SK, Gurkan U, Patel R, Bonomo RA, Draz M. 3D Printed Materials for Combating Antimicrobial Resistance. MATERIALS TODAY (KIDLINGTON, ENGLAND) 2023; 67:371-398. [PMID: 37790286 PMCID: PMC10545363 DOI: 10.1016/j.mattod.2023.05.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Three-dimensional (3D) printing is a rapidly growing technology with a significant capacity for translational applications in both biology and medicine. 3D-printed living and non-living materials are being widely tested as a potential replacement for conventional solutions for testing and combating antimicrobial resistance (AMR). The precise control of cells and their microenvironment, while simulating the complexity and dynamics of an in vivo environment, provides an excellent opportunity to advance the modeling and treatment of challenging infections and other health conditions. 3D-printing models the complicated niches of microbes and host-pathogen interactions, and most importantly, how microbes develop resistance to antibiotics. In addition, 3D-printed materials can be applied to testing and delivering antibiotics. Here, we provide an overview of 3D printed materials and biosystems and their biomedical applications, focusing on ever increasing AMR. Recent applications of 3D printing to alleviate the impact of AMR, including developed bioprinted systems, targeted bacterial infections, and tested antibiotics are presented.
Collapse
Affiliation(s)
- Mert Tunca Doganay
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Cyril John Chelliah
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Abdullah Tozluyurt
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | | | - Umut Gurkan
- Mechanical and Aerospace Engineering Department, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology and Division of Public Health, Infectious Diseases, and Occupational medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH, USA
| | - Mohamed Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
- Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biomedical Engineering, Cleveland Clinic, Cleveland, OH 44106, USA
| |
Collapse
|
20
|
Witzany C, Rolff J, Regoes RR, Igler C. The pharmacokinetic-pharmacodynamic modelling framework as a tool to predict drug resistance evolution. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001368. [PMID: 37522891 PMCID: PMC10433423 DOI: 10.1099/mic.0.001368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023]
Abstract
Pharmacokinetic-pharmacodynamic (PKPD) models, which describe how drug concentrations change over time and how that affects pathogen growth, have proven highly valuable in designing optimal drug treatments aimed at bacterial eradication. However, the fast rise of antimicrobial resistance calls for increased focus on an additional treatment optimization criterion: avoidance of resistance evolution. We demonstrate here how coupling PKPD and population genetics models can be used to determine treatment regimens that minimize the potential for antimicrobial resistance evolution. Importantly, the resulting modelling framework enables the assessment of resistance evolution in response to dynamic selection pressures, including changes in antimicrobial concentration and the emergence of adaptive phenotypes. Using antibiotics and antimicrobial peptides as an example, we discuss the empirical evidence and intuition behind individual model parameters. We further suggest several extensions of this framework that allow a more comprehensive and realistic prediction of bacterial escape from antimicrobials through various phenotypic and genetic mechanisms.
Collapse
Affiliation(s)
| | - Jens Rolff
- Evolutionary Biology, Institute for Biology, Freie Universität Berlin, Berlin, Germany
| | - Roland R. Regoes
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Claudia Igler
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- School of Biological Sciences, University of Manchester, Manchester, UK
| |
Collapse
|
21
|
Feng M, Namanja-Magliano H, Rajagopalan S, Mishra T, Ducati RG, Hirsch BM, Kelly L, Szymczak W, Fajardo JE, Sidoli S, Fiser A, Jacobs WR, Schramm VL. MAT Gain of Activity Mutation in Helicobacter pylori Is Associated with Resistance to MTAN Transition State Analogues. ACS Infect Dis 2023; 9:966-978. [PMID: 36920074 DOI: 10.1021/acsinfecdis.2c00644] [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: 03/16/2023]
Abstract
Helicobacter pylori is found in the gut lining of more than half of the world's population, causes gastric ulcers, and contributes to stomach cancers. Menaquinone synthesis in H. pylori relies on the rare futalosine pathway, where H. pylori 5'-methylthioadenosine nucleosidase (MTAN) is proposed to play an essential role. Transition state analogues of MTAN, including BuT-DADMe-ImmA (BTDIA) and MeT-DADMe-ImmA (MTDIA), exhibit bacteriostatic action against numerous diverse clinical isolates of H. pylori with minimum inhibitory concentrations (MIC's) of <2 ng/mL. Three H. pylori BTDIA-resistant clones were selected under increasing BTDIA pressure. Whole genome sequencing showed no mutations in MTAN. Instead, resistant clones had mutations in metK, methionine adenosyltransferase (MAT), feoA, a regulator of the iron transport system, and flhF, a flagellar synthesis regulator. The mutation in metK causes expression of a MAT with increased catalytic activity, leading to elevated cellular S-adenosylmethionine. Metabolite analysis and the mutations associated with resistance suggest multiple inputs associated with BTDIA resistance. Human gut microbiome exposed to MTDIA revealed no growth inhibition under aerobic or anaerobic conditions. Transition state analogues of H. pylori MTAN have potential as agents for treating H. pylori infection without disruption of the human gut microbiome or inducing resistance in the MTAN target.
Collapse
Affiliation(s)
- Mu Feng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Hilda Namanja-Magliano
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Saranathan Rajagopalan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Tanmay Mishra
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Rodrigo G Ducati
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Brett M Hirsch
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Libusha Kelly
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States.,Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Wendy Szymczak
- Department of Pathology, Montefiore-Einstein Medical Center, Bronx, New York 10467, United States
| | - Jorge Eduardo Fajardo
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| |
Collapse
|
22
|
Saini M, Gaurav A, Kothari A, Omar BJ, Gupta V, Bhattacharjee A, Pathania R. Small Molecule IITR00693 (2-Aminoperimidine) Synergizes Polymyxin B Activity against Staphylococcus aureus and Pseudomonas aeruginosa. ACS Infect Dis 2023; 9:692-705. [PMID: 36716174 DOI: 10.1021/acsinfecdis.2c00622] [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: 01/31/2023]
Abstract
The rise of antibiotic resistance among skin-infecting pathogens poses an urgent threat to public health and has fueled the search for new therapies. Enhancing the potency of currently used antibiotics is an alternative for the treatment of infections caused by drug-resistant pathogens. In this study, we aimed to identify a small molecule that can potentiate currently used antibiotics. IITR00693 (2-aminoperimidine), a novel antibacterial small molecule, potentiates the antibacterial activity of polymyxin B against Staphylococcus aureus and Pseudomonas aeruginosa. Herein, we investigated in detail the mode of action of this interaction and the molecule's capability to combat soft-tissue infections caused by S. aureus and P. aeruginosa. A microdilution checkerboard assay was performed to determine the synergistic interaction between polymyxin B and IITR00693 in clinical isolates of S. aureus and P. aeruginosa. Time-kill kinetics, post-antibiotic effect, and resistance generation studies were performed to assess the pharmacodynamics of the combination. Assays based on different fluorescent probes were performed to decipher the mechanism of action of this combination. The in vivo efficacy of the IITR00693-polymyxin B combination was determined in a murine acute wound infection model. IITR00693 exhibited broad-spectrum antibacterial activity. IITR00693 potentiated polymyxin B and colistin against polymyxin-resistant S. aureus. IITR00693 prevented the generation of resistant mutants against multiple antibiotics. The IITR00693-polymyxin B combination decreased the S. aureus count by >3 log10 CFU in a murine acute wound infection model. IITR00693 is a potential and promising candidate for the treatment of soft-tissue infections along with polymyxins.
Collapse
Affiliation(s)
- Mahak Saini
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand247 667, India
| | - Amit Gaurav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand247 667, India
| | - Ashish Kothari
- Department of Microbiology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand249 201, India
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand249 201, India
| | - Varsha Gupta
- Department of Microbiology, Government Medical College and Hospital Chandigarh, Chandigarh160 030, India
| | | | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand247 667, India
| |
Collapse
|
23
|
Fernandes S, Gomes IB, Simões M. Antimicrobial and antibiofilm potentiation by a triple combination of dual biocides and a phytochemical with complementary activity. Food Res Int 2023; 167:112680. [PMID: 37087211 DOI: 10.1016/j.foodres.2023.112680] [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: 12/05/2022] [Revised: 01/26/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023]
Abstract
The failure of current sanitation practices requires the development of effective solutions for microbial control. Although combinations using antibiotics have been extensively studied to look for additive/synergistic effects, biocide combinations are still underexplored. This study aims to evaluate the antimicrobial effectiveness of dual biocide and triple biocide/phytochemical combinations, where phytochemicals are used as quorum sensing (QS) inhibitors. The biocides selected were benzalkonium chloride (BAC) and peracetic acid (PAA) - as commonly used biocides, and glycolic acid (GA) and glyoxal (GO) - as alternative and sustainable biocides. Curcumin (CUR) and 10-undecenoic acid (UA) were the phytochemicals selected, based on their QS inhibition properties. A checkerboard assay was used for the screening of chemical interactions based on the cell growth inhibitory effects against Bacilluscereus and Pseudomonasfluorescens. It was observed that dual biocide combinations resulted in indifference, except the PAA + GA combination, which had a potential additive effect. PAA + GA + CUR and PAA + GA + UA combinations also triggered additive effects. The antimicrobial effects of the combinations were further evaluated on the inactivation of planktonic and biofilm cells after 30 min of exposure. These experiments corroborated the checkerboard results, in which PAA + GA was the most effective combination against planktonic cells (additive/synergistic effects). The antimicrobial effects of triple combinations were species- and biocide-specific. While CUR only potentiate the antimicrobial activity of GA against B.cereus, GA + UA and PAA + GA + UA combinations promoted additional antimicrobial effects against both bacteria. Biofilms were found to be highly tolerant, with modest antimicrobial effects being observed for all the combinations tested. However, this study demonstrated that low doses of biocides can be effective in bacterial control when combining biocides with a QS inhibitor, in particular, the combination of the phytochemical UA (as a QS inhibitor) with GA and PAA.
Collapse
Affiliation(s)
- Susana Fernandes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Inês B Gomes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Manuel Simões
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
| |
Collapse
|
24
|
Abstract
Almost all bactericidal drugs require bacterial replication and/or metabolic activity for their killing activity. When these processes are inhibited by bacteriostatic antibiotics, bacterial killing is significantly reduced. One notable exception is the lipopeptide antibiotic daptomycin, which has been reported to efficiently kill growth-arrested bacteria. However, these studies employed only short periods of growth arrest (<1 h), which may not fully represent the duration of growth arrest that can occur in vivo. We found that a growth inhibitory concentration of the protein synthesis inhibitor tetracycline led to a time-dependent induction of daptomycin tolerance in S. aureus, with an approximately 100,000-fold increase in survival after 16 h of growth arrest, relative to exponential-phase bacteria. Daptomycin tolerance required glucose and was associated with increased production of the cell wall polymers peptidoglycan and wall-teichoic acids. However, while the accumulation of peptidoglycan was required for daptomycin tolerance, only a low abundance of wall teichoic acid was necessary. Therefore, whereas tolerance to most antibiotics occurs passively due to a lack of metabolic activity and/or replication, daptomycin tolerance arises via active cell wall remodelling. IMPORTANCE Understanding why antibiotics sometimes fail to cure infections is fundamental to improving treatment outcomes. This is a major challenge when it comes to Staphylococcus aureus because this pathogen causes several different chronic or recurrent infections. Previous work has shown that a lack of replication, as often occurs during infection, makes bacteria tolerant of most bactericidal antibiotics. However, one antibiotic that has been reported to kill nonreplicating bacteria is daptomycin. In this work, we show that the growth arrest of S. aureus does in fact lead to daptomycin tolerance, but it requires time, nutrients, and biosynthetic pathways, making it distinct from other types of antibiotic tolerance that occur in nonreplicating bacteria.
Collapse
|
25
|
Therapeutic Options and Outcomes for the Treatment of Children with Gram-Positive Bacteria with Resistances of Concern: A Systematic Review. Antibiotics (Basel) 2023; 12:antibiotics12020261. [PMID: 36830174 PMCID: PMC9952189 DOI: 10.3390/antibiotics12020261] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/14/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA), methicillin-resistant coagulase-negative Staphylococci (MR-CoNS), and vancomycin-resistant Enterococci (VRE) are increasing worldwide and represent a threat for the limited treatment options in pediatric patients and neonates compared to adults. Recommendations in pediatrics are mainly extrapolated from adults' studies. METHODS A literature search for the treatment of these pathogens in children (<18 years old) was conducted in Embase, MEDLINE, and Cochrane Library. Studies reporting data on single-patient-level outcomes related to a specific antibiotic treatment for multidrug resistant (MDR) Gram-positive bacterial infection in children were included. Studies reporting data from adults and children were included if single-pediatric-level information could be identified (PROSPERO registration: CRD42022383867). RESULTS The search identified 11,740 studies (since January 2000), of which 48 fulfilled both the inclusion and the exclusion criteria and were included in the analysis: 29 for MRSA, 20 for VRE, and seven for MR-CoNS. Most studies were retrospective studies. Vancomycin was mainly used as a comparator, while linezolid and daptomycin were the most studied antimicrobials showing good efficacy. CONCLUSIONS Linezolid showed a safety and efficacy profile in a neonatal setting; daptomycin is increasingly used for MRSA, but the evidence is scarce for VRE.
Collapse
|
26
|
Munir S, Khurshid M, Ahmad M, Ashfaq UA, Zaki MEA. Exploring the Antimicrobial and Pharmacological Potential of NF22 as a Potent Inhibitor of E. coli DNA Gyrase: An In Vitro and In Silico Study. Pharmaceutics 2022; 14:pharmaceutics14122768. [PMID: 36559262 PMCID: PMC9784730 DOI: 10.3390/pharmaceutics14122768] [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: 09/25/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Toward the search for novel antimicrobial agents to control pathogenic E. coli-associated infections, a series of novel norfloxacin derivatives were screened for antimicrobial activities. The norfloxacin derivative, 1-ethyl-6-fluoro-7-(4-(2-(2-(3-hydroxybenzylidene)hydrazinyl)-2-oxoethyl)piperazin-1-yl)-4-oxo-1,4-dihydroquinoline-3-carboxylic acid (NF22) demonstrated excellent antibacterial activities against E. coli ATCC 25922 (MIC = 0.0625 μg/mL) and MDR E. coli 1-3 (MIC = 1, 2 and 1 µg/mL). The time-kill kinetic studies have demonstrated that the NF22 was advantageous over norfloxacin and ciprofloxacin in killing the control and MDR E. coli strains. The checkerboard assay showed that NF22 in combination with tetracycline had a synergistic effect against the E. coli strains. The experimental findings are supported by molecular modeling studies on DNA gyrase, explaining the interactions involved for compound NF22, compared to norfloxacin and ciprofloxacin. Further, the compound was also evaluated for various pharmacokinetics (absorption, metabolism, distribution, toxicity and excretion) as well as drug-likeness properties. Our data have highlighted the potential of norfloxacin by restoring its efficacy against E. coli which could lead to the development of new antimicrobial agents.
Collapse
Affiliation(s)
- Samman Munir
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad 38000, Pakistan
- Correspondence: (U.A.A.); (M.E.A.Z.)
| | - Magdi E. A. Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
- Correspondence: (U.A.A.); (M.E.A.Z.)
| |
Collapse
|
27
|
Ganesan S, Alagarasan JK, Sonaimuthu M, Aruchamy K, Alkallas FH, Ben Gouider Trabelsi A, Kusmartsev FV, Polisetti V, Lee M, Lo HM. Preparation and Characterization of Salsalate-Loaded Chitosan Nanoparticles: In Vitro Release and Antibacterial and Antibiofilm Activity. Mar Drugs 2022; 20:md20120733. [PMID: 36547880 PMCID: PMC9785770 DOI: 10.3390/md20120733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
The controlled-release characteristic of drug delivery systems is utilized to increase the residence time of therapeutic agents in the human body. This study aimed to formulate and characterize salsalate (SSL)-loaded chitosan nanoparticles (CSNPs) prepared using the ionic gelation method and to assess their in vitro release and antibacterial and antibiofilm activities. The optimized CSNPs and CSNP-SSL formulation were characterized for particle size (156.4 ± 12.7 nm and 132.8 ± 17.4 nm), polydispersity index (0.489 ± 0.011 and 0.236 ± 132 0.021), zeta potential (68 ± 16 mV and 37 ± 11 mV), and entrapment efficiency (68.9 ± 2.14%). Physicochemical features of these nanoparticles were characterized using UV-visible and Fourier transform infrared spectroscopy and X-ray diffraction pattern. Scanning electron microscopy studies indicated that CSNPs and CSNP-SSL were spherical in shape with a smooth surface and their particle size ranged between 200 and 500 nm. In vitro release profiles of the optimized formulations showed an initial burst followed by slow and sustained drug release after 18 h (64.2 ± 3.2%) and 48 h (84.6 ± 4.23%), respectively. Additionally, the CSNPs and CSNP-SSL nanoparticles showed a sustained antibacterial action against Staphylococcus aureus (15.7 ± 0.1 and 19.1 ± 1.2 mm) and Escherichia coli (17.5 ± 0.8 and 21.6 ± 1.7 243 mm). Interestingly, CSNP-SSL showed better capability (89.4 ± 1.2% and 95.8 ± 0.7%) than did CSNPs in inhibiting antibiofilm production by Enterobacter tabaci (E2) and Klebsiella quasipneumoniae (SC3). Therefore, CSNPs are a promising dosage form for sustained drug delivery and enhanced antibacterial and antibiofilm activity of SSL; these results could be translated into increased patient compliance.
Collapse
Affiliation(s)
- Sivarasan Ganesan
- Department of Environmental Engineering and Management, Chaoyang University of Technology, Taichung 41349, Taiwan
| | | | - Mohandoss Sonaimuthu
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Kanakaraj Aruchamy
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Fatemah Homoud Alkallas
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Amira Ben Gouider Trabelsi
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Fedor Vasilievich Kusmartsev
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
- Department of Physics, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates
| | - Veerababu Polisetti
- Wallenberg Wood Science Center, Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-100 44 Stockholm, Sweden
- Correspondence: (V.P.); (M.L.); (H.-M.L.)
| | - Moonyong Lee
- School of Chemical Engineering, Yeungnam University, Gyeongsan 38541, Republic of Korea
- Correspondence: (V.P.); (M.L.); (H.-M.L.)
| | - Huang-Mu Lo
- Department of Environmental Engineering and Management, Chaoyang University of Technology, Taichung 41349, Taiwan
- Correspondence: (V.P.); (M.L.); (H.-M.L.)
| |
Collapse
|
28
|
Antibiotic combinations reduce Staphylococcus aureus clearance. Nature 2022; 610:540-546. [PMID: 36198788 PMCID: PMC9533972 DOI: 10.1038/s41586-022-05260-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 08/22/2022] [Indexed: 12/17/2022]
Abstract
The spread of antibiotic resistance is attracting increased attention to combination-based treatments. Although drug combinations have been studied extensively for their effects on bacterial growth1–11, much less is known about their effects on bacterial long-term clearance, especially at cidal, clinically relevant concentrations12–14. Here, using en masse microplating and automated image analysis, we systematically quantify Staphylococcus aureus survival during prolonged exposure to pairwise and higher-order cidal drug combinations. By quantifying growth inhibition, early killing and longer-term population clearance by all pairs of 14 antibiotics, we find that clearance interactions are qualitatively different, often showing reciprocal suppression whereby the efficacy of the drug mixture is weaker than any of the individual drugs alone. Furthermore, in contrast to growth inhibition6–10 and early killing, clearance efficacy decreases rather than increases as more drugs are added. However, specific drugs targeting non-growing persisters15–17 circumvent these suppressive effects. Competition experiments show that reciprocal suppressive drug combinations select against resistance to any of the individual drugs, even counteracting methicillin-resistant Staphylococcus aureus both in vitro and in a Galleria mellonella larva model. As a consequence, adding a β-lactamase inhibitor that is commonly used to potentiate treatment against β-lactam-resistant strains can reduce rather than increase treatment efficacy. Together, these results underscore the importance of systematic mapping the long-term clearance efficacy of drug combinations for designing more-effective, resistance-proof multidrug regimes. Different pairs of antibiotics show qualitatively different bacterial clearance interactions—some pairs show reciprocal suppression whereby the drug mixture efficacy is weaker than the individual drugs alone, and the clearance efficacy decreases as more drugs are added.
Collapse
|
29
|
Erdogan Eliuz EA, Yabalak E, Gökşen G, Ayas D. Chemical composition, antifungal activity, antifungal mechanism and interaction manner of the fatty acid of Prunus mahaleb L. with fluconazole. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:2337-2349. [PMID: 34382873 DOI: 10.1080/09603123.2021.1963686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The interaction manner of Prunus mahaleb L. (P. mahaleb) seed oil (MSO) and fluconazole (FLC: antimycotic) combinations (MSO*FLC) against C. albicans and C. parapsilosis were evaluated using the microdilution technique. The most representative compounds of mahaleb oil were found to be conjugated linolenic acid (34.39%), oleic acid (31.76%), and linoleic acid (25.54%) by GC-MS. In antimicrobial activity study, P. mahaleb had an inhibition zone (IZ) of C. albicans and C. parapsilosis with 6.89 mm and 11.39 mm and a minimum inhibitory concentration (MIC) with 35.3 µgmL-1 and 23.9 µgmL-1, respectively. The strongest indifferent effect was observed as 57.14% for C. albicans and 100% for C. parapsilosis in fluconazole-mahaleb oil combinations. An increase in DNA and protein leakage was observed when yeast was exposed to the FA. The destruction on the cell surface was visualized using Scanning Electron Microscopy (SEM) analysis.
Collapse
Affiliation(s)
- Elif Ayşe Erdogan Eliuz
- Department of Food Technology, Mersin University, Vocational School of Technical Sciences, Mersin, Turkey
| | - Erdal Yabalak
- Department of Chemistry, Mersin University, Faculty of Arts and Science, Mersin, Turkey
- Department of Nanotechnology and Advanced Materials, Mersin University, Mersin, Turkey
| | - Gülden Gökşen
- Department of Food Engineering, Mersin University, Mersin, Turkey
| | - Deniz Ayas
- Department of Seafood Processing Technology, Mersin University, Mersin, Turkey
| |
Collapse
|
30
|
Arip M, Selvaraja M, R M, Tan LF, Leong MY, Tan PL, Yap VL, Chinnapan S, Tat NC, Abdullah M, K D, Jubair N. Review on Plant-Based Management in Combating Antimicrobial Resistance - Mechanistic Perspective. Front Pharmacol 2022; 13:879495. [PMID: 36249774 PMCID: PMC9557208 DOI: 10.3389/fphar.2022.879495] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial resistance (AMR) occurs when microbes no longer respond to any pharmacological agents, rendering the conventional antimicrobial agents ineffective. AMR has been classified as one of the top 10 life-threatening global health problems needed multilevel attention and global cooperation to attain the Sustainable Development Goals (SDGs) according to the World Health Organization (WHO), making the discovery of a new and effective antimicrobial agent a priority. The recommended treatments for drug-resistant microbes are available but limited. Furthermore, the transformation of microbes over time increases the risk of developing drug resistance. Hence, plant metabolites such as terpenes, phenolic compounds and alkaloids are widely studied due to their antibacterial, antiviral, antifungal and antiparasitic effects. Plant-derived antimicrobials are preferred due to their desirable efficacy and safety profile. Plant metabolites work by targeting microbial cell membranes, interfering with the synthesis of microbial DNA/RNA/enzymes and disrupting quorum sensing and efflux pump expression. They also work synergistically with conventional antibiotics to enhance antimicrobial effects. Accordingly, this review aims to identify currently available pharmacological therapies against microbes and AMR, as well as to discuss the importance of plant and secondary metabolites as a possible solution for AMR together with their mechanisms of action. All the information was obtained from government databases, WHO websites, PubMed, Springer, Google Scholar and Science Direct. Based on the information obtained, AMR is regarded as a significant warning to global healthcare. Plant derivatives such as secondary metabolites may be considered as potential therapeutic targets to mitigate the non-ending AMR.
Collapse
Affiliation(s)
- Masita Arip
- Allergy and Immunology Research Centre, Institute for Medical Research, Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Malarvili Selvaraja
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, Malaysia
- *Correspondence: Malarvili Selvaraja, ; Mogana R,
| | - Mogana R
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, Malaysia
- *Correspondence: Malarvili Selvaraja, ; Mogana R,
| | - Lee Fang Tan
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, Malaysia
| | - Mun Yee Leong
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, Malaysia
| | - Puay Luan Tan
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, Malaysia
| | - Vi Lien Yap
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, Malaysia
| | - Sasikala Chinnapan
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, Malaysia
| | - Ng Chin Tat
- Immunology Unit, Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Maha Abdullah
- Immunology Unit, Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Dharmendra K
- Narayan Institute of Pharmacy, Gopal Narayan Singh University, Jamuhar, India
| | - Najwan Jubair
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, Malaysia
| |
Collapse
|
31
|
Tsai CE, Yang CJ, Chuang YC, Wang JT, Sheng WH, Chen YC, Chang SC. Evaluation of the synergistic effect of ceftaroline against methicillin-resistant Staphylococcus aureus. Int J Infect Dis 2022; 122:230-236. [PMID: 35640827 DOI: 10.1016/j.ijid.2022.05.057] [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: 02/24/2022] [Revised: 04/22/2022] [Accepted: 05/25/2022] [Indexed: 10/18/2022] Open
Abstract
OBJECTIVES We aimed to determine the synergistic effects of ceftaroline (CPT) in combination with daptomycin (DAP), vancomycin (VAN), or linezolid (LNZ) against various methicillin-resistant Staphylococcus aureus (MRSA) strains. METHODS MRSA strains randomly selected from 2014 to 2018 were studied. Checkerboard titration and in vitro time-kill analyses were used to determine the synergistic activities of the antibiotic combinations. RESULTS A total of 10 genetically distinct MRSA strains were included in this study. The checkerboard titration analysis revealed that the CPT-DAP, CPT-VAN, and CPT-LNZ combinations had a synergistic effect against 30%, 10%, and 10% of the selected MRSA strains, respectively. Using time-kill analysis, we showed that CPT-DAP exhibited a significant synergistic and sustained bactericidal effect against both DAP-susceptible (Δ colony-forming units/ml, -5.79; P = 0.0495) and DAP-resistant (Δ colony-forming units/ml, -6.40; P = 0.0463) MRSA strains at a concentration of 0.5 × the minimum inhibitory concentration of CPT plus 0.5 × the minimum inhibitory concentration of DAP. No synergistic bactericidal effects were observed for the CPT-VAN and CPT-LNZ combinations against the selected strains. CONCLUSION The CPT-DAP combination showed better synergistic activity than the CPT-VAN and CPT-LNZ combinations against the enrolled MRSA strains. DAP, rather than VAN or LNZ, might be a better choice for CPT combination in the treatment of MRSA infections.
Collapse
Affiliation(s)
- Cheng-En Tsai
- School of Medicine, National Taiwan University College of Medicine, Taipei City, Taiwan
| | - Chia-Jui Yang
- Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan; School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Chung Chuang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan.
| | - Jann-Tay Wang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
| | - Wang-Huei Sheng
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
| | - Yee-Chun Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
| | - Shan-Chwen Chang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei City, Taiwan
| |
Collapse
|
32
|
Hemez C, Clarelli F, Palmer AC, Bleis C, Abel S, Chindelevitch L, Cohen T, Abel zur Wiesch P. Mechanisms of antibiotic action shape the fitness landscapes of resistance mutations. Comput Struct Biotechnol J 2022; 20:4688-4703. [PMID: 36147681 PMCID: PMC9463365 DOI: 10.1016/j.csbj.2022.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/15/2022] Open
Abstract
Antibiotic-resistant pathogens are a major public health threat. A deeper understanding of how an antibiotic's mechanism of action influences the emergence of resistance would aid in the design of new drugs and help to preserve the effectiveness of existing ones. To this end, we developed a model that links bacterial population dynamics with antibiotic-target binding kinetics. Our approach allows us to derive mechanistic insights on drug activity from population-scale experimental data and to quantify the interplay between drug mechanism and resistance selection. We find that both bacteriostatic and bactericidal agents can be equally effective at suppressing the selection of resistant mutants, but that key determinants of resistance selection are the relationships between the number of drug-inactivated targets within a cell and the rates of cellular growth and death. We also show that heterogeneous drug-target binding within a population enables resistant bacteria to evolve fitness-improving secondary mutations even when drug doses remain above the resistant strain's minimum inhibitory concentration. Our work suggests that antibiotic doses beyond this "secondary mutation selection window" could safeguard against the emergence of high-fitness resistant strains during treatment.
Collapse
Affiliation(s)
- Colin Hemez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Graduate Program in Biophysics, Harvard University, Boston, MA 02115, USA
- Corresponding authors at: Broad Institute, 75 Ames St, Room 3035, Cambridge, MA 02412, USA (C. Hemez). Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway (P. Abel zur Wiesch).
| | - Fabrizio Clarelli
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Adam C. Palmer
- Department of Pharmacology, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christina Bleis
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sören Abel
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Division of Infection Control, Norwegian Institute of Public Health, Oslo 0318, Norway
| | - Leonid Chindelevitch
- Department of Infectious Disease Epidemiology, Imperial College, London SW7 2AZ, UK
| | - Theodore Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Pia Abel zur Wiesch
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Division of Infection Control, Norwegian Institute of Public Health, Oslo 0318, Norway
- Corresponding authors at: Broad Institute, 75 Ames St, Room 3035, Cambridge, MA 02412, USA (C. Hemez). Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway (P. Abel zur Wiesch).
| |
Collapse
|
33
|
McNeil MB, Cheung CY, Waller NJE, Adolph C, Chapman CL, Seeto NEJ, Jowsey W, Li Z, Hameed HMA, Zhang T, Cook GM. Uncovering interactions between mycobacterial respiratory complexes to target drug-resistant Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:980844. [PMID: 36093195 PMCID: PMC9461714 DOI: 10.3389/fcimb.2022.980844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/03/2022] [Indexed: 11/24/2022] Open
Abstract
Mycobacterium tuberculosis remains a leading cause of infectious disease morbidity and mortality for which new drug combination therapies are needed. Mycobacterial bioenergetics has emerged as a promising space for the development of novel therapeutics. Further to this, unique combinations of respiratory inhibitors have been shown to have synergistic or synthetic lethal interactions, suggesting that combinations of bioenergetic inhibitors could drastically shorten treatment times. Realizing the full potential of this unique target space requires an understanding of which combinations of respiratory complexes, when inhibited, have the strongest interactions and potential in a clinical setting. In this review, we discuss (i) chemical-interaction, (ii) genetic-interaction and (iii) chemical-genetic interaction studies to explore the consequences of inhibiting multiple mycobacterial respiratory components. We provide potential mechanisms to describe the basis for the strongest interactions. Finally, whilst we place an emphasis on interactions that occur with existing bioenergetic inhibitors, by highlighting interactions that occur with alternative respiratory components we envision that this information will provide a rational to further explore alternative proteins as potential drug targets and as part of unique drug combinations.
Collapse
Affiliation(s)
- Matthew B. McNeil
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins, Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- *Correspondence: Matthew B. McNeil, ; Gregory M. Cook,
| | - Chen-Yi Cheung
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Natalie J. E. Waller
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Cara Adolph
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Cassandra L. Chapman
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Noon E. J. Seeto
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - William Jowsey
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Zhengqiu Li
- School of Pharmacy, Jinan University, Guangzhou, China
| | - H. M. Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
- China-New Zealand Joint Laboratory of Biomedicine and Health, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
- Guangdong-Hong Kong-Macau Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Gregory M. Cook
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Maurice Wilkins, Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
- *Correspondence: Matthew B. McNeil, ; Gregory M. Cook,
| |
Collapse
|
34
|
Barnes KB, Richards MI, Burgess G, Armstrong SJ, Bentley C, Maishman TC, Laws TR, Nelson M, Harding SV. Investigation of a combination therapy approach for the treatment of melioidosis. Front Microbiol 2022; 13:934312. [PMID: 36051754 PMCID: PMC9424925 DOI: 10.3389/fmicb.2022.934312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
The efficacy of finafloxacin as a component of a layered defense treatment regimen was determined in vitro and in vivo against an infection with Burkholderia pseudomallei. Doxycycline was down-selected from a panel of antibiotics evaluated in vitro and used in combination with finafloxacin in a Balb/c mouse model of inhalational melioidosis. When treatment was initiated at 24 h post-infection with B. pseudomallei, there were no differences in the level of protection offered by finafloxacin or doxycycline (as monotherapies) when compared to the combination therapy. There was evidence for improved bacterial control in the groups treated with finafloxacin (as monotherapies or in combination with doxycycline) when compared to mice treated with doxycycline. Survival comparisons of finafloxacin and doxycycline (as monotherapies) or in combination initiated at 36 h post-infection indicated that finafloxacin was superior to doxycycline. Doxycycline was also unable to control the levels of bacteria within tissues to the extent that doxycycline and finafloxacin used in combination or finafloxacin (as a sole therapy) could. In summary, finafloxacin is a promising therapy for use in the event of exposure to B. pseudomallei.
Collapse
Affiliation(s)
- Kay B. Barnes
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Mark I. Richards
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Gary Burgess
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Stuart J. Armstrong
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | | | - Thomas C. Maishman
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Thomas R. Laws
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Michelle Nelson
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
| | - Sarah V. Harding
- Defence Science and Technology Laboratory, Porton Down, Salisbury, United Kingdom
- Department of Respiratory Sciences, University of Leicester, Leicester, United Kingdom
| |
Collapse
|
35
|
Lv J, Liu G, Hao J, Ju Y, Sun B, Sun Y. Computational models, databases and tools for antibiotic combinations. Brief Bioinform 2022; 23:6652783. [PMID: 35915052 DOI: 10.1093/bib/bbac309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Antibiotic combination is a promising strategy to extend the lifetime of antibiotics and thereby combat antimicrobial resistance. However, screening for new antibiotic combinations is both time-consuming and labor-intensive. In recent years, an increasing number of researchers have used computational models to predict effective antibiotic combinations. In this review, we summarized existing computational models for antibiotic combinations and discussed the limitations and challenges of these models in detail. In addition, we also collected and summarized available data resources and tools for antibiotic combinations. This study aims to help computational biologists design more accurate and interpretable computational models.
Collapse
Affiliation(s)
- Ji Lv
- College of Computer Science and Technology, Jilin University, Changchun, China.,Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Guixia Liu
- College of Computer Science and Technology, Jilin University, Changchun, China.,Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Junli Hao
- College of Food Science, Northeast Agricultural University, Harbin, China
| | - Yuan Ju
- Sichuan University Library, Sichuan University, Chengdu, China
| | - Binwen Sun
- Engineering Research Center for New Materials and Precision Treatment Technology of Malignant Tumor Therapy, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ying Sun
- Department of Respiratory Medicine, the First Hospital of Jilin University, Changchun, China
| |
Collapse
|
36
|
Ma X, Fu S, Wang Y, Zhao L, Yu W, He Y, Ni W, Gao Z. Proteomics Study of the Synergistic Killing of Tigecycline in Combination With Aminoglycosides Against Carbapenem-Resistant Klebsiella pneumoniae. Front Cell Infect Microbiol 2022; 12:920761. [PMID: 35846751 PMCID: PMC9280366 DOI: 10.3389/fcimb.2022.920761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/18/2022] [Indexed: 11/14/2022] Open
Abstract
Co-administration of antibiotics with synergistic effects is one method to combat carbapenem-resistant organisms. Although the synergistic effects of tigecycline combined with aminoglycosides against carbapenem-resistant Klebsiella pneumoniae (CRKP) have been demonstrated in vitro and in animal models, the underlying mechanism remains elusive. Here we used proteomics analysis to assess the short-term bacterial responses to tigecycline and aminoglycosides alone or in combination. Emergence of tigecycline resistance during treatment and the susceptibility of tigecycline-resistant strains to aminoglycosides was further evaluated. The proteomic responses to tigecycline and aminoglycosides were divergent in monotherapy, with proteomic alterations to combination therapy dominated by tigecycline. Adaptive responses to tigecycline were associated with the upregulation of oxidative phosphorylation and translation-related proteins. These responses might confer CRKP hypersensitivity towards aminoglycosides by increasing the drug uptake and binding targets. Meanwhile, tigecycline might perturb adaptive responses to aminoglycosides through inhibition of heat shock response. Tigecycline-resistant strains could be isolated within 24 h exposure even in strains without heteroresistance, and the sensitivity to aminoglycosides significantly increased in resistant strains. Overall, these findings demonstrated that adaption to tigecycline in CRKP was a double-edged sword associated with the synergistic killing in tigecycline–aminoglycoside combination. Evolutionary hypersensitivity can provide novel insight into the mechanisms of antibiotic synergistic effects.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Wentao Ni
- *Correspondence: Wentao Ni, ; Zhancheng Gao,
| | | |
Collapse
|
37
|
Yang J, Barra JT, Fung DK, Wang JD. Bacillus subtilis produces (p)ppGpp in response to the bacteriostatic antibiotic chloramphenicol to prevent its potential bactericidal effect. MLIFE 2022; 1:101-113. [PMID: 38817674 PMCID: PMC10989873 DOI: 10.1002/mlf2.12031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/24/2022] [Indexed: 06/01/2024]
Abstract
Antibiotics combat bacteria through their bacteriostatic (by growth inhibition) or bactericidal (by killing bacteria) action. Mechanistically, it has been proposed that bactericidal antibiotics trigger cellular damage, while bacteriostatic antibiotics suppress cellular metabolism. Here, we demonstrate how the difference between bacteriostatic and bactericidal activities of the antibiotic chloramphenicol can be attributed to an antibiotic-induced bacterial protective response: the stringent response. Chloramphenicol targets the ribosome to inhibit the growth of the Gram-positive bacterium Bacillus subtilis. Intriguingly, we found that chloramphenicol becomes bactericidal in B. subtilis mutants unable to produce (p)ppGpp. We observed a similar (p)ppGpp-dependent bactericidal effect of chloramphenicol in the Gram-positive pathogen Enterococcus faecalis. In B. subtilis, chloramphenicol treatment induces (p)ppGpp accumulation through the action of the (p)ppGpp synthetase RelA. (p)ppGpp subsequently depletes the intracellular concentration of GTP and antagonizes GTP action. This GTP regulation is critical for preventing chloramphenicol from killing B. subtilis, as bypassing (p)ppGpp-dependent GTP regulation potentiates chloramphenicol killing, while reducing GTP synthesis increases survival. Finally, chloramphenicol treatment protects cells from the classical bactericidal antibiotic vancomycin, reminiscent of the clinical phenomenon of antibiotic antagonism. Taken together, our findings suggest a role of (p)ppGpp in the control of the bacteriostatic and bactericidal activity of antibiotics in Gram-positive bacteria, which can be exploited to potentiate the efficacy of existing antibiotics.
Collapse
Affiliation(s)
- Jin Yang
- Department of BacteriologyUniversity of WisconsinMadisonUSA
| | | | - Danny K. Fung
- Department of BacteriologyUniversity of WisconsinMadisonUSA
| | - Jue D. Wang
- Department of BacteriologyUniversity of WisconsinMadisonUSA
| |
Collapse
|
38
|
The physiology and genetics of bacterial responses to antibiotic combinations. Nat Rev Microbiol 2022; 20:478-490. [PMID: 35241807 DOI: 10.1038/s41579-022-00700-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2022] [Indexed: 02/08/2023]
Abstract
Several promising strategies based on combining or cycling different antibiotics have been proposed to increase efficacy and counteract resistance evolution, but we still lack a deep understanding of the physiological responses and genetic mechanisms that underlie antibiotic interactions and the clinical applicability of these strategies. In antibiotic-exposed bacteria, the combined effects of physiological stress responses and emerging resistance mutations (occurring at different time scales) generate complex and often unpredictable dynamics. In this Review, we present our current understanding of bacterial cell physiology and genetics of responses to antibiotics. We emphasize recently discovered mechanisms of synergistic and antagonistic drug interactions, hysteresis in temporal interactions between antibiotics that arise from microbial physiology and interactions between antibiotics and resistance mutations that can cause collateral sensitivity or cross-resistance. We discuss possible connections between the different phenomena and indicate relevant research directions. A better and more unified understanding of drug and genetic interactions is likely to advance antibiotic therapy.
Collapse
|
39
|
Coram MA, Wang L, Godinez WJ, Barkan DT, Armstrong Z, Ando DM, Feng BY. Morphological Characterization of Antibiotic Combinations. ACS Infect Dis 2022; 8:66-77. [PMID: 34937332 DOI: 10.1021/acsinfecdis.1c00312] [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: 11/29/2022]
Abstract
Combination therapies are common in many therapeutic contexts, including infectious diseases and cancer. A common approach for evaluating combinations in vitro is to assess effects on cell growth as synergistic, antagonistic, or neutral using "checkerboard" experiments to systematically sample combinations of agents in multiple doses. To further understand the effects of antibiotic combinations, we employed high-content imaging to study the morphological changes caused by combination treatments in checkerboard experiments. Using an automated, unsupervised image analysis approach to group morphologies, and an "expert-in-the-loop" to annotate them, we attributed the heterogeneous morphological changes ofEscherichia coli cells to varying doses of both single-agent and combination treatments. We identified patterns of morphological change, including morphological potentiation, competition, and the emergence of unexpected morphologies. We found these frequently did not correlate with synergistic or antagonistic effects on viability, suggesting morphological approaches may provide a distinctive signature of the biological interaction between compounds over a range of conditions. Among the unexpected morphologies we observed, there were transitional changes associated with intermediate doses of compounds and uncharacterized phenotypes associated with well-studied antibiotics. Our approach exemplifies how unsupervised image analysis and expert knowledge can be combined to reckon with complex phenotypic changes arising from combination screening, dose titrations, or polypharmacology. In this way, quantification of morphological diversity across treatment conditions could aid in analysis and prioritization of complementary pairings of antibiotic agents by more closely capturing the true signature of the integrated cellular response.
Collapse
Affiliation(s)
- Marc A. Coram
- Google Research Applied Science, Mountain View, California 94043, United States
| | - Lisha Wang
- Infectious Diseases, Novartis Institutes for BioMedical Research, Inc., Emeryville, California 94608, United States
| | - William J. Godinez
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Inc., Emeryville, California 94608, United States
| | - David T. Barkan
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Inc., Emeryville, California 94608, United States
| | - Zan Armstrong
- Google Research Applied Science, Mountain View, California 94043, United States
| | - D. Michael Ando
- Google Research Applied Science, Mountain View, California 94043, United States
| | - Brian Y. Feng
- Infectious Diseases, Novartis Institutes for BioMedical Research, Inc., Emeryville, California 94608, United States
| |
Collapse
|
40
|
Teo JQM, Fauzi N, Ho JJY, Tan SH, Lee SJY, Lim TP, Cai Y, Chang HY, Mohamed Yusoff N, Sim JHC, Tan TT, Ong RTH, Kwa ALH. In vitro Bactericidal Activities of Combination Antibiotic Therapies Against Carbapenem-Resistant Klebsiella pneumoniae With Different Carbapenemases and Sequence Types. Front Microbiol 2022; 12:779988. [PMID: 34970239 PMCID: PMC8713045 DOI: 10.3389/fmicb.2021.779988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) is becoming increasingly problematic due to the limited effectiveness of new antimicrobials or other factors such as treatment cost. Thus, combination therapy remains a suitable treatment option. We aimed to evaluate the in vitro bactericidal activity of various antibiotic combinations against CRKP with different carbapenemase genotypes and sequence types (STs). Thirty-seven CRKP with various STs and carbapenemases were exposed to 11 antibiotic combinations (polymyxin B or tigecycline in combination with β-lactams including aztreonam, cefepime, piperacillin/tazobactam, doripenem, meropenem, and polymyxin B with tigecycline) in static time-kill studies (TKS) using clinically achievable concentrations. Out of the 407 isolate-combination pairs, only 146 (35.8%) were bactericidal (≥3 log10CFU/mL decrease from initial inoculum). Polymyxin B in combination with doripenem, meropenem, or cefepime was the most active, each demonstrating bactericidal activity in 27, 24, and 24 out of 37 isolates, respectively. Tigecycline in combination with β-lactams was rarely bactericidal. Aside from the lower frequency of bactericidal activity in the dual-carbapenemase producers, there was no apparent difference in combination activity among the strains with other carbapenemase types. In addition, bactericidal combinations were varied even in strains with similar STs, carbapenemases, and other genomic characteristics. Our findings demonstrate that the bactericidal activity of antibiotic combinations is highly strain-specific likely owing to the complex interplay of carbapenem-resistance mechanisms, i.e., carbapenemase genotype alone cannot predict in vitro bactericidal activity. The availability of WGS information can help rationalize the activity of certain combinations. Further studies should explore the use of genomic markers with phenotypic information to predict combination activity.
Collapse
Affiliation(s)
- Jocelyn Qi-Min Teo
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Nazira Fauzi
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Jayden Jun-Yuan Ho
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Si Hui Tan
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | | | - Tze Peng Lim
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore.,Singhealth Duke-NUS Pathology Academic Clinical Programme, Singapore, Singapore.,Singhealth Duke-NUS Medicine Academic Clinical Programme, Singapore, Singapore
| | - Yiying Cai
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | - Hong Yi Chang
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore
| | | | | | - Thuan Tong Tan
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Andrea Lay-Hoon Kwa
- Department of Pharmacy, Singapore General Hospital, Singapore, Singapore.,Singhealth Duke-NUS Medicine Academic Clinical Programme, Singapore, Singapore.,Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
| |
Collapse
|
41
|
Vatankhah M, Khosravi K, Zargar N, Shirvani A, Nekoofar MH, Dianat O. Antibacterial efficacy of antibiotic pastes versus calcium hydroxide intracanal dressing: A systematic review and meta-analysis of ex vivo studies. J Conserv Dent 2022; 25:463-480. [PMID: 36506621 PMCID: PMC9733540 DOI: 10.4103/jcd.jcd_183_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/15/2022] [Accepted: 05/20/2022] [Indexed: 12/15/2022] Open
Abstract
Background Conflicting findings on the potency of antibiotic pastes versus calcium hydroxide (CH) have been evident in the literature. Aims To compare the antibacterial efficacy of single antibiotic paste (SAP), double antibiotic paste (DAP), triple antibiotic paste (TAP), and modified TAP (mTAP) with CH on bacterial biofilms. Methods PubMed, Scopus, and Embase were comprehensively searched until August 23, 2021. The study protocol was registered in the PROSPERO. Ex vivo studies performed on Enterococcus faecalis or polymicrobial biofilms incubated on human/bovine dentin were selected. The quality of the studies was assessed using a customized quality assessment tool. Standardized mean difference (SMD) with a 95% confidence interval (CI) was calculated for the meta-analysis. Meta-regression models were used to identify the sources of heterogeneity and to compare the efficacy of pastes. Results The qualitative and quantitative synthesis included 40 and 23 papers, respectively, out of 1421 search results. TAP (SMD = -3.82; CI, -5.44 to -2.21; P < 0.001) and SAPs (SMD = -2.38; CI, -2.81 to - 1.94; P < 0.001) had significantly higher antibacterial efficacy compared to the CH on E. faecalis biofilm. However, no significant difference was found between the efficacy of DAP (SMD = -2.74; CI, -5.56-0.07; P = 0.06) or mTAP (SMD = -0.28; CI, -0.82-0.26; P = 0.31) and CH. Meta-regression model on E. faecalis showed that SAPs have similar efficacy compared to TAP and significantly better efficacy than DAP. On dual-species (SMD = 0.15; CI, -1.00-1.29; P = 0.80) or multi-species (SMD = 0.23; CI, -0.08-0.55; P = 0.15) biofilms, DAP and CH had similar efficacy. Conclusions Ex vivo evidence showed that antibiotic pastes were either superior or equal to CH. The studied SAPs had considerably higher or similar antibacterial effectiveness compared to DAP, CH, and TAP. Hence, combined antibiotic therapy was not necessarily required for root canal disinfection ex vivo.
Collapse
Affiliation(s)
- Mohammadreza Vatankhah
- Iranian Center for Endodontic Research, Research Institute of Dental Sciences, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kamyar Khosravi
- Iranian Center for Endodontic Research, Research Institute of Dental Sciences, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nazanin Zargar
- Department of Endodontics, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Armin Shirvani
- Iranian Center for Endodontic Research, Research Institute of Dental Sciences, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Omid Dianat
- Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, Maryland, USA,Address for correspondence: Dr. Omid Dianat, Division of Endodontics, Department of Advanced Oral Sciences and Therapeutics, School of Dentistry, University of Maryland, Baltimore, 650 West Baltimore Street, 4th Floor, Baltimore, MD 21201, USA. E-mail:
| |
Collapse
|
42
|
Abstract
In the struggle with antibiotic resistance, we are losing. There is now a serious threat of moving into a postantibiotic world. High levels of resistance, in terms of both frequency and strength, have evolved against all clinically approved antibiotics worldwide. The usable life span of new clinically approved antibiotics is typically less than a decade before resistance reaches frequencies so high as to require only guarded usage. However, microbes have produced antibiotics for millennia without resistance becoming an existential issue. If resistance is the inevitable consequence of antibiotic usage, as has been the human experience, why has it not become an issue for microbes as well, especially since resistance genes are as prevalent in nature as the genes responsible for antibiotic production? Here, we ask how antibiotics can exist given the almost ubiquitous presence of resistance genes in the very microbes that have produced and used antibiotics since before humans walked the planet. We find that the context of both production and usage of antibiotics by microbes may be key to understanding how resistance is managed over time, with antibiotic synthesis and resistance existing in a paired relationship, much like a cipher and key, that impacts microbial community assembly. Finally, we put forward the cohesive, ecologically based "secret society" hypothesis to explain the longevity of antibiotics in nature.
Collapse
Affiliation(s)
- Fabrizio Spagnolo
- Biology Department, Queens College of The City University of New York, Flushing, New York, USA
| | - Monica Trujillo
- Department of Biological Sciences and Geology, Queensborough Community College, The City University of New York, Bayside, New York, USA
| | - John J. Dennehy
- Biology Department, Queens College of The City University of New York, Flushing, New York, USA
- The Graduate Center of The City University of New York, New York, New York, USA
| |
Collapse
|
43
|
Consequential drug combinations for tuberculosis treatments. Cell Syst 2021; 12:1021-1022. [PMID: 34793699 DOI: 10.1016/j.cels.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Improved therapies for tuberculosis will require the careful revision of complex, multi-drug regimens. In this issue of Cell Systems, Larkins-Ford et al. integrate extensive dose-response measurements of drug combinations, in vivo animal data, and computational analysis to provide a new predictive framework for the prioritization of specific antitubercular drug regimens.
Collapse
|
44
|
Danis-Wlodarczyk KM, Cai A, Chen A, Gittrich MR, Sullivan MB, Wozniak DJ, Abedon ST. Friends or Foes? Rapid Determination of Dissimilar Colistin and Ciprofloxacin Antagonism of Pseudomonas aeruginosa Phages. Pharmaceuticals (Basel) 2021; 14:1162. [PMID: 34832944 PMCID: PMC8624478 DOI: 10.3390/ph14111162] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/14/2022] Open
Abstract
Phage therapy is a century-old technique employing viruses (phages) to treat bacterial infections, and in the clinic it is often used in combination with antibiotics. Antibiotics, however, interfere with critical bacterial metabolic activities that can be required by phages. Explicit testing of antibiotic antagonism of phage infection activities, though, is not a common feature of phage therapy studies. Here we use optical density-based 'lysis-profile' assays to assess the impact of two antibiotics, colistin and ciprofloxacin, on the bactericidal, bacteriolytic, and new-virion-production activities of three Pseudomonas aeruginosa phages. Though phages and antibiotics in combination are more potent in killing P. aeruginosa than either acting alone, colistin nevertheless substantially interferes with phage bacteriolytic and virion-production activities even at its minimum inhibitory concentration (1× MIC). Ciprofloxacin, by contrast, has little anti-phage impact at 1× or 3× MIC. We corroborate these results with more traditional measures, particularly colony-forming units, plaque-forming units, and one-step growth experiments. Our results suggest that ciprofloxacin could be useful as a concurrent phage therapy co-treatment especially when phage replication is required for treatment success. Lysis-profile assays also appear to be useful, fast, and high-throughput means of assessing antibiotic antagonism of phage infection activities.
Collapse
Affiliation(s)
| | - Alice Cai
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| | - Anna Chen
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| | - Marissa R. Gittrich
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel J. Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA;
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| |
Collapse
|
45
|
Qi Q, Angermayr SA, Bollenbach T. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Front Microbiol 2021; 12:760017. [PMID: 34745067 PMCID: PMC8564399 DOI: 10.3389/fmicb.2021.760017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/30/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding interactions between antibiotics used in combination is an important theme in microbiology. Using the interactions between the antifolate drug trimethoprim and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model, we applied a transcriptomic approach for dissecting interactions between two antibiotics with different modes of action. When trimethoprim and erythromycin were combined, the transcriptional response of genes from the sulfate reduction pathway deviated from the dominant effect of trimethoprim on the transcriptome. We successfully altered the drug interaction from additivity to suppression by increasing the sulfate level in the growth environment and identified sulfate reduction as an important metabolic determinant that shapes the interaction between the two drugs. Our work highlights the potential of using prioritization of gene expression patterns as a tool for identifying key metabolic determinants that shape drug-drug interactions. We further demonstrated that the sigma factor-binding protein gene crl shapes the interactions between the two antibiotics, which provides a rare example of how naturally occurring variations between strains of the same bacterial species can sometimes generate very different drug interactions.
Collapse
Affiliation(s)
- Qin Qi
- Institute of Science and Technology Austria, Klosterneuburg, Austria.,Institute for Biological Physics, University of Cologne, Cologne, Germany
| | | | - Tobias Bollenbach
- Institute for Biological Physics, University of Cologne, Cologne, Germany.,Center for Data and Simulation Science, University of Cologne, Cologne, Germany
| |
Collapse
|
46
|
Vázquez K, Vanegas P, Cruzat C, Novoa N, Arrué R, Vanegas E. Antibacterial and Antifungal Properties of Electrospun Recycled PET Polymeric Fibers Functionalized with Zinc Oxide Nanoparticles. Polymers (Basel) 2021; 13:3763. [PMID: 34771320 PMCID: PMC8587058 DOI: 10.3390/polym13213763] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 01/27/2023] Open
Abstract
Currently, to reduce the environmental problems associated with plastic waste, methods are being sought to use this waste as raw materials in different applications, such as fibers. In addition, to improve these materials and provide different properties, nanoparticles (NPs) are incorporated. In the present work, polymeric fibers made of recycled polyethylene terephthalate (r-PET) from post-consumer water bottles, functionalized with 0%, 1.5%, 3% and 6% zinc oxide nanoparticles (ZnO-NPs) in function of r-PET weight, were elaborated to evaluate their antibacterial and antifungal characteristics. The ZnO-NPs were synthesized by the solvothermal method, obtaining particles with a mean diameter of 38.15 nm, while the fibers were obtained by electrospinning with a diameter range between 200-5000 nm. The functionalized fibers were carried out against Escherichia coli and Bacillus subtilis through the agar diffusion method, obtaining the highest inhibition halo at 6% w/w ZnO-NPs, being 26.5 mm and 34.25 mm, respectively. In addition, the same method was used to evaluate the antifungal activity of Penicillium s.p. and Fusarium graminearum, observing antifungal properties due to the presence of nanoparticles in the fibers.
Collapse
Affiliation(s)
- Katherine Vázquez
- Chemical Engineering, Faculty of Chemical Sciences, University of Cuenca, Cuenca 010203, Ecuador;
| | - Paul Vanegas
- Department of Space and Population, Faculty of Chemical Sciences, University of Cuenca, Cuenca 010203, Ecuador;
| | - Christian Cruzat
- Center for Environmental Studies, Department of Applied Chemisty and Production Systems, Faculty of Chemical Sciences, University of Cuenca, Cuenca 010203, Ecuador;
| | - Néstor Novoa
- Laboratorio de Química Inorgánica y Organometálica, Departamento de Química Analítica e Inorgánica, Facultad de Ciencias Químicas, Universidad de Concepción, Edmundo Larenas 129, Casilla 160-C, Concepción 4070386, Chile; (N.N.); (R.A.)
| | - Ramón Arrué
- Laboratorio de Química Inorgánica y Organometálica, Departamento de Química Analítica e Inorgánica, Facultad de Ciencias Químicas, Universidad de Concepción, Edmundo Larenas 129, Casilla 160-C, Concepción 4070386, Chile; (N.N.); (R.A.)
| | - Eulalia Vanegas
- Center for Environmental Studies, Department of Applied Chemisty and Production Systems, Faculty of Chemical Sciences, University of Cuenca, Cuenca 010203, Ecuador;
| |
Collapse
|
47
|
A personalised approach to antibiotic pharmacokinetics and pharmacodynamics in critically ill patients. Anaesth Crit Care Pain Med 2021; 40:100970. [PMID: 34728411 DOI: 10.1016/j.accpm.2021.100970] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/26/2021] [Accepted: 08/14/2021] [Indexed: 01/01/2023]
Abstract
Critically ill patients admitted to intensive care unit (ICU) with severe infections, or those who develop nosocomial infections, have poor outcomes with substantial morbidity and mortality. Such patients commonly have suboptimal antibiotic exposures at routinely used antibiotic doses related to an increased volume of distribution and altered clearance due to their underlying altered physiology. Furthermore, the use of extracorporeal devices such as renal replacement therapy and extracorporeal membrane oxygenation in these group of patients also has the potential to alter in vivo drug concentrations. Moreover, ICU patients are likely to be infected with less-susceptible pathogens. Therefore, one potential contributing cause to the poor outcomes observed in critically ill patients may be related to subtherapeutic antibiotic exposures. Newer concepts include the clinician considering optimised dosing based on a blood antibiotic exposure defined by pharmacokinetic modelling and therapeutic drug monitoring, combined with a knowledge of the antibiotic penetration into the site of infection, thereby achieving optimal bacterial killing. Such optimised dosing is likely to improve patient outcomes. The aim of this review is to highlight key aspects of antibiotic pharmacokinetics and pharmacodynamics (PK/PD) in critically ill patients and provide a PK/PD approach to tailor antibiotic dosing to the individual patient.
Collapse
|
48
|
White K, Nicoletti G, Cornell H. Antibacterial Profile of a Microbicidal Agent Targeting Tyrosine Phosphatases and Redox Thiols, Novel Drug Targets. Antibiotics (Basel) 2021; 10:1310. [PMID: 34827248 PMCID: PMC8615086 DOI: 10.3390/antibiotics10111310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 10/23/2021] [Accepted: 10/24/2021] [Indexed: 11/16/2022] Open
Abstract
The activity profile of a protein tyrosine phosphatase (PTP) inhibitor and redox thiol oxidant, nitropropenyl benzodioxole (NPBD), was investigated across a broad range of bacterial species. In vitro assays assessed inhibitory and lethal activity patterns, the induction of drug variants on long term exposure, the inhibitory interactions of NPBD with antibiotics, and the effect of plasma proteins and redox thiols on activity. A literature review indicates the complexity of PTP and redox signaling and suggests likely metabolic targets. NPBD was broadly bactericidal to pathogens of the skin, respiratory, urogenital and intestinal tracts. It was effective against antibiotic resistant strains and slowly replicating and dormant cells. NPBD did not induce resistant or drug-tolerant phenotypes and showed low cross reactivity with antibiotics in synergy assays. Binding to plasma proteins indicated lowered in-vitro bioavailability and reduction of bactericidal activity in the presence of thiols confirmed the contribution of thiol oxidation and oxidative stress to lethality. This report presents a broad evaluation of the antibacterial effect of PTP inhibition and redox thiol oxidation, illustrates the functional diversity of bacterial PTPs and redox thiols, and supports their consideration as novel targets for antimicrobial drug development. NPBD is a dual mechanism agent with an activity profile which supports consideration of tyrosine phosphatases and bacterial antioxidant systems as promising targets for drug development.
Collapse
Affiliation(s)
- Kylie White
- STEM College, RMIT University, Melbourne, VIC 3001, Australia; (G.N.); (H.C.)
| | | | | |
Collapse
|
49
|
Alfonseca-Silva E, Cruz-Villa JC, Gutiérrez L, Sumano H. Successful treatment of recurrent subclinical mastitis in cows caused by enrofloxacin resistant bacteria by means of the sequential intramammary infusion of enrofloxacin HCl-2H 2O and ceftiofur HCl: a clinical trial. J Vet Sci 2021; 22:e78. [PMID: 34697924 PMCID: PMC8636650 DOI: 10.4142/jvs.2021.22.e78] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/19/2021] [Accepted: 08/29/2021] [Indexed: 11/28/2022] Open
Abstract
Background Recurrent subclinical mastitis (RScM) due to resistant bacteria has low clinical and bacteriological cure rates, often requiring the culling of cows. The sequential intra-mammary administration of enrofloxacin hydrochloride-dihydrate (enro-C) followed by ceftiofur HCl may be useful for treating these cases. Objectives This study assessed the bacteriological and clinical cure-efficacies of the sequentially intramammary administration of enro-C, followed by ceftiofur HCl to treat RScM in Holstein/Friesian cows. Methods This trial was conducted in a herd with a high prevalence of RScM, and 20 Holstein/Friesian cows were included: 45% suffering subclinical mastitis and 38.9% of the mammary quarters affected. Twenty-nine bacterial isolates in vitro resistant to enro-C were obtained (coagulase-negative Staphylococcus spp, 55.2%; Staphylococcus aureus, 27.6%; Escherichia coli, 6.9%; Streptococcus uberis, 6.9%; Corynebacterium bovis, 3.4%). Polymerase chain reaction-isolated the following genes linked to enro-C resistance: chromosomal (gyrA) and plasmid (aac(6')-lb-cr). The treatments were as follows: twice-daily intramammary infusions of enro-C (300 mg/10 mL) for 5 days. Cows clinically considered treatment failures were also treated with intramammary ceftiofur (125 mg/10 mL, twice daily for 5 days. The clinical and bacteriological cure rates were carried out when completing each treatment phase and at 14 and 21 days, aided by a California mastitis test, somatic cell count, and failure to identify the initially causative bacteria. Results Enro-C achieved 65% clinical and bacteriological cure rates, and 100% cure rates were obtained after the rescue treatment with ceftiofur HCl. Conclusions Outstanding clinical and bacteriological cure rates in cows affected by RScM were achieved with the consecutive intramammary infusions of enro-C, followed by ceftiofur HCl.
Collapse
Affiliation(s)
- Edgar Alfonseca-Silva
- Department of Microbiology and Immunology, School of Veterinary Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Juan Carlos Cruz-Villa
- Department of Microbiology and Immunology, School of Veterinary Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Lilia Gutiérrez
- Department of Physiology and Pharmacology, School of Veterinary Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Hector Sumano
- Department of Physiology and Pharmacology, School of Veterinary Medicine, National Autonomous University of Mexico, Mexico City 04510, Mexico.
| |
Collapse
|
50
|
Husain DR, Wardhani R. Antibacterial activity of endosymbiotic bacterial compound from Pheretima sp. earthworms inhibit the growth of Salmonella Typhi and Staphylococcus aureus: in vitro and in silico approach. IRANIAN JOURNAL OF MICROBIOLOGY 2021; 13:537-543. [PMID: 34557283 PMCID: PMC8421580 DOI: 10.18502/ijm.v13i4.6981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background and Objectives: Earthworms coexist with various pathogenic microorganisms; thus, their immunity mechanisms have developed through a long process of adaptation, including through endogenous bacterial symbionts. This study aims to identify earthworm endosymbiont bacteria compounds and their antibacterial activity through an in vitro approach supported by an in silico approach. Materials and Methods: This research was conducted using the in vitro inhibition test through agar diffusion and the in silico test using molecular docking applications, namely, PyRx and Way2Drugs Prediction of Activity Spectra for Substances (PASS). Results: The in vitro results showed a potent inhibition activity with a clear zone diameter of 21.75 and 15.5 mm for Staphylococcus aureus and Salmonella Typhi, respectively. These results are supported by chromatography and in silico tests, which showed that several compounds in endosymbiotic bacteria, cyclo (phenylalanyl-prolyl) and sedanolide, have high binding affinity values with several antibiotic-related target proteins in both pathogenic bacteria. Cyclo (phenylalanyl-prolyl) has the highest binding affinity of −6.0 to dihydropteroate synthase, −8.2 to topoisomerase, and −8.2 to the outer membrane, whereas sedanolide has the highest binding affinity to DNA gyrase with approximately −7.3. This antibiotic activity was also clarified through the Way2Drugs PASS application. Conclusion: Ten active compounds of endosymbiont bacteria, Cyclo (phenylalanyl-prolyl) and sedanolide were potential candidates for antibacterial compounds based on the inhibition test of the agar diffusion method and the results of reverse docking and Way2Drugs PASS.
Collapse
Affiliation(s)
- Dirayah Rauf Husain
- Department of Biology, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia
| | - Riuh Wardhani
- Department of Biology, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia
| |
Collapse
|