1
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Tran TA, Sridhar S, Reece ST, Lunguya O, Jacobs J, Van Puyvelde S, Marks F, Dougan G, Thomson NR, Nguyen BT, Bao PT, Baker S. Combining machine learning with high-content imaging to infer ciprofloxacin susceptibility in isolates of Salmonella Typhimurium. Nat Commun 2024; 15:5074. [PMID: 38871710 PMCID: PMC11176356 DOI: 10.1038/s41467-024-49433-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 06/05/2024] [Indexed: 06/15/2024] Open
Abstract
Antimicrobial resistance (AMR) is a growing public health crisis that requires innovative solutions. Current susceptibility testing approaches limit our ability to rapidly distinguish between antimicrobial-susceptible and -resistant organisms. Salmonella Typhimurium (S. Typhimurium) is an enteric pathogen responsible for severe gastrointestinal illness and invasive disease. Despite widespread resistance, ciprofloxacin remains a common treatment for Salmonella infections, particularly in lower-resource settings, where the drug is given empirically. Here, we exploit high-content imaging to generate deep phenotyping of S. Typhimurium isolates longitudinally exposed to increasing concentrations of ciprofloxacin. We apply machine learning algorithms to the imaging data and demonstrate that individual isolates display distinct growth and morphological characteristics that cluster by time point and susceptibility to ciprofloxacin, which occur independently of ciprofloxacin exposure. Using a further set of S. Typhimurium clinical isolates, we find that machine learning classifiers can accurately predict ciprofloxacin susceptibility without exposure to it or any prior knowledge of resistance phenotype. These results demonstrate the principle of using high-content imaging with machine learning algorithms to predict drug susceptibility of clinical bacterial isolates. This technique may be an important tool in understanding the morphological impact of antimicrobials on the bacterial cell to identify drugs with new modes of action.
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Affiliation(s)
- Tuan-Anh Tran
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sushmita Sridhar
- The Department of Medicine, University of Cambridge, Cambridge, UK
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Stephen T Reece
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Sanofi, Kymab, Babraham Research Campus, Cambridge, UK
| | - Octavie Lunguya
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
- Service de Microbiologie, Cliniques Universitaires de Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Jan Jacobs
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sandra Van Puyvelde
- The Department of Medicine, University of Cambridge, Cambridge, UK
- Laboratory of Medical Microbiology, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Florian Marks
- The Department of Medicine, University of Cambridge, Cambridge, UK
- International Vaccine Institute, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | - Gordon Dougan
- The Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nicholas R Thomson
- The Wellcome Sanger Institute, Hinxton, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Binh T Nguyen
- Faculty of Mathematics and Computer Science, University of Science, Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Pham The Bao
- Information Science Faculty, Saigon University, Ho Chi Minh City, Vietnam
| | - Stephen Baker
- The Department of Medicine, University of Cambridge, Cambridge, UK.
- IAVI, Chelsea and Westminster Hospital, London, UK.
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2
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Schäfer AB, Sidarta M, Abdelmesseh Nekhala I, Marinho Righetto G, Arshad A, Wenzel M. Dissecting antibiotic effects on the cell envelope using bacterial cytological profiling: a phenotypic analysis starter kit. Microbiol Spectr 2024; 12:e0327523. [PMID: 38289933 PMCID: PMC10913488 DOI: 10.1128/spectrum.03275-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Phenotypic analysis assays such as bacterial cytological profiling (BCP) have become increasingly popular for antibiotic mode of action analysis. A plethora of dyes, protein fusions, and reporter strains are available and have been used for this purpose, enabling both rapid mode of action categorization and in-depth analysis of antibiotic mechanisms. However, non-expert researchers may struggle choosing suitable assays and interpreting results. This is a particular problem for antibiotics that have multiple or complex targets, such as the bacterial cell envelope. Here, we set out to curate a minimal set of accessible and affordable phenotypic assays that allow distinction between membrane and cell wall targets, can identify dual-action inhibitors, and can be implemented in most research environments. To this end, we employed BCP, membrane potential, fluidity, and cell wall synthesis assays. To assess specificity and ease of interpretation, we tested three well-characterized and commercially available reference antibiotics: the potassium ionophore valinomycin, the lipid II-binding glycopeptide vancomycin, and the dual-action lantibiotic nisin, which binds lipid II and forms a membrane pore. Based on our experiments, we suggest a minimal set of BCP, a membrane-potentiometric probe, and fluorescent protein fusions to MinD and MreB as basic assay set and recommend complementing these assays with Laurdan-based fluidity measurements and a PliaI reporter fusion, where indicated. We believe that our results can provide guidance for researchers who wish to use phenotypic analysis for mode of action studies but do not possess the specialized equipment or expert knowledge to employ the full breadth of possible techniques.IMPORTANCEPhenotypic analysis assays using specialized fluorescence fusions and dyes have become increasingly popular in antibiotic mode of action analysis. However, it can be difficult to implement these methods due to the need for specialized equipment and/or the complexity of bacterial cell biology and physiology, making the interpretation of results difficult for non-experts. This is especially problematic for compounds that have multiple or pleiotropic effects, such as inhibitors of the bacterial cell envelope. In order to make phenotypic analysis assays accessible to labs, whose primary expertise is not bacterial cell biology, or with limited equipment and resources, a set of simple and broadly accessible assays is needed that is easy to implement, execute, and interpret. Here, we have curated a set of assays and strains that does not need highly specialized equipment, can be performed in most labs, and is straightforward to interpret without knowing the intricacies of bacterial cell biology.
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Affiliation(s)
- Ann-Britt Schäfer
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Margareth Sidarta
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Ireny Abdelmesseh Nekhala
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Gabriela Marinho Righetto
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
| | - Aysha Arshad
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, Sweden
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3
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Sakoulas G, Nizet V. Measuring beta-lactam minimum inhibitory concentrations in Staphylococcus aureus in the clinical microbiology laboratory: pinning the tail on the donkey. J Clin Microbiol 2024; 62:e0036623. [PMID: 37966224 PMCID: PMC10793257 DOI: 10.1128/jcm.00366-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
Significant shortcomings have been identified in standard methods of susceptibility testing in bacteriological media, not only because the media fails to recapitulate the in vivo environment, but susceptibility testing itself fails to capture sub-MIC effects that significantly attenuate bacterial virulence properties. Until susceptibility testing conditions better recapitulate the in vivo environment, attempts to establish the quantitative relevance of beta-lactam MIC using current clinical microbiology standards in Staphylococcus aureus infections will likely prove unsuccessful.
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Affiliation(s)
- George Sakoulas
- Sharp Rees-Stealy Medical Group, San Diego, California, USA
- UCSD School of Medicine, La Jolla, California, USA
| | - Victor Nizet
- UCSD School of Medicine, La Jolla, California, USA
- Skaggs School of Pharmacy, UCSD School of Medicine, La Jolla, California, USA
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4
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Kamal El-Sagheir AM, Abdelmesseh Nekhala I, Abd El-Gaber MK, Aboraia AS, Persson J, Schäfer AB, Wenzel M, Omar FA. Rational design, synthesis, molecular modeling, biological activity, and mechanism of action of polypharmacological norfloxacin hydroxamic acid derivatives. RSC Med Chem 2023; 14:2593-2610. [PMID: 38099058 PMCID: PMC10718593 DOI: 10.1039/d3md00309d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/11/2023] [Indexed: 12/17/2023] Open
Abstract
Fluoroquinolones are broad-spectrum antibiotics that target gyrase and topoisomerase IV, involved in DNA compaction and segregation. We synthesized 28 novel norfloxacin hydroxamic acid derivatives with additional metal-chelating and hydrophobic pharmacophores, designed to enable interactions with additional drug targets. Several compounds showed equal or better activity than norfloxacin against Gram-positive, Gram-negative, and mycobacteria, with MICs as low as 0.18 μM. The most interesting derivatives were selected for in silico, in vitro, and in vivo mode of action studies. Molecular docking, enzyme inhibition, and bacterial cytological profiling confirmed inhibition of gyrase and topoisomerase IV for all except two tested derivatives (10f and 11f). Further phenotypic analysis revealed polypharmacological effects on peptidoglycan synthesis for four derivatives (16a, 17a, 17b, 20b). Interestingly, compounds 17a, 17b, and 20b, showed never seen before effects on cell wall synthetic enzymes, including MreB, MurG, and PonA, suggesting a novel mechanism of action, possibly impairing the lipid II cycle.
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Affiliation(s)
| | - Ireny Abdelmesseh Nekhala
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
| | | | - Ahmed S Aboraia
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
| | - Jonatan Persson
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Ann-Britt Schäfer
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology 412 96 Gothenburg Sweden
- Center for Antibiotic Resistance Research in Gothenburg (CARe) Gothenburg Sweden
| | - Farghaly A Omar
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
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5
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Boyang H, Yangyanqiu W, Wenting R, Chenxin Y, Jian C, Zhanbo Q, Yanjun Y, Qiang Y, Shuwen H. Application and progress of highcontent imaging in molecular biology. Biotechnol J 2023; 18:e2300170. [PMID: 37639283 DOI: 10.1002/biot.202300170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/03/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Humans have adopted many different methods to explore matter imaging, among which high content imaging (HCI) could conduct automated imaging analysis of cells while maintaining its structural and functional integrity. Meanwhile, as one of the most important research tools for diagnosing human diseases, HCI is widely used in the frontier of medical research, and its future application has attracted researchers' great interests. Here, the meaning of HCI was briefly explained, the history of optical imaging and the birth of HCI were described, and the experimental methods of HCI were described. Furthermore, the directions of the application of HCI were highlighted in five aspects: protein localization changes, gene identification, chemical and genetic analysis, microbiology, and drug discovery. Most importantly, some challenges and future directions of HCI were discussed, and the application and optimization of HCI were expected to be further explored.
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Affiliation(s)
- Hu Boyang
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Wang Yangyanqiu
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Rui Wenting
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Yan Chenxin
- Shulan International Medical School, Zhejiang Shuren University, Hangzhou, China
| | - Chu Jian
- Fifth Affiliated Clinical Medical College of Zhejiang Chinese Medical University, Huzhou Central Hospital, Huzhou, China
| | - Qu Zhanbo
- Fifth Affiliated Clinical Medical College of Zhejiang Chinese Medical University, Huzhou Central Hospital, Huzhou, China
| | - Yao Yanjun
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Yan Qiang
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Han Shuwen
- Huzhou Hospital of Zhejiang University, Affiliated Central Hospital Huzhou University, Huzhou, China
- Key Laboratory of Multiomics Research and Clinical Transformation of Digestive Cancer of Huzhou, Huzhou, China
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6
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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7
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Zagajewski A, Turner P, Feehily C, El Sayyed H, Andersson M, Barrett L, Oakley S, Stracy M, Crook D, Nellåker C, Stoesser N, Kapanidis AN. Deep learning and single-cell phenotyping for rapid antimicrobial susceptibility detection in Escherichia coli. Commun Biol 2023; 6:1164. [PMID: 37964031 PMCID: PMC10645916 DOI: 10.1038/s42003-023-05524-4] [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: 02/02/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023] Open
Abstract
The rise of antimicrobial resistance (AMR) is one of the greatest public health challenges, already causing up to 1.2 million deaths annually and rising. Current culture-based turnaround times for bacterial identification in clinical samples and antimicrobial susceptibility testing (AST) are typically 18-24 h. We present a novel proof-of-concept methodological advance in susceptibility testing based on the deep-learning of single-cell specific morphological phenotypes directly associated with antimicrobial susceptibility in Escherichia coli. Our models can reliably (80% single-cell accuracy) classify untreated and treated susceptible cells for a lab-reference fully susceptible E. coli strain, across four antibiotics (ciprofloxacin, gentamicin, rifampicin and co-amoxiclav). For ciprofloxacin, we demonstrate our models reveal significant (p < 0.001) differences between bacterial cell populations affected and unaffected by antibiotic treatment, and show that given treatment with a fixed concentration of 10 mg/L over 30 min these phenotypic effects correlate with clinical susceptibility defined by established clinical breakpoints. Deploying our approach on cell populations from six E. coli strains obtained from human bloodstream infections with varying degrees of ciprofloxacin resistance and treated with a range of ciprofloxacin concentrations, we show single-cell phenotyping has the potential to provide equivalent information to growth-based AST assays, but in as little as 30 min.
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Affiliation(s)
- Alexander Zagajewski
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Piers Turner
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Conor Feehily
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Hafez El Sayyed
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Monique Andersson
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Lucinda Barrett
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Sarah Oakley
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Mathew Stracy
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Derrick Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK
| | - Christoffer Nellåker
- Nuffield Department of Women's & Reproductive Health, University of Oxford, Big Data Institute, Oxford, OX3 7LF, UK.
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
- Department of Microbiology and Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK.
| | - Achillefs N Kapanidis
- Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK.
- Kavli Institute for Nanoscience Discovery, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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8
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Baranova AA, Tyurin AP, Korshun VA, Alferova VA. Sensing of Antibiotic-Bacteria Interactions. Antibiotics (Basel) 2023; 12:1340. [PMID: 37627760 PMCID: PMC10451291 DOI: 10.3390/antibiotics12081340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Sensing of antibiotic-bacteria interactions is an important area of research that has gained significant attention in recent years. Antibiotic resistance is a major public health concern, and it is essential to develop new strategies for detecting and monitoring bacterial responses to antibiotics in order to maintain effective antibiotic development and antibacterial treatment. This review summarizes recent advances in sensing strategies for antibiotic-bacteria interactions, which are divided into two main parts: studies on the mechanism of action for sensitive bacteria and interrogation of the defense mechanisms for resistant ones. In conclusion, this review provides an overview of the present research landscape concerning antibiotic-bacteria interactions, emphasizing the potential for method adaptation and the integration of machine learning techniques in data analysis, which could potentially lead to a transformative impact on mechanistic studies within the field.
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Affiliation(s)
| | | | | | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (A.P.T.); (V.A.K.)
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9
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Wang C, Nguyen T, Yang X, Mellick GD, Feng Y. Phytochemical investigation of Asarum sieboldii var. seoulense and the phenotypic profiles of its constituents against a Parkinson's Disease olfactory cell line. Bioorg Med Chem Lett 2023; 92:129386. [PMID: 37355024 DOI: 10.1016/j.bmcl.2023.129386] [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: 05/05/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 06/26/2023]
Abstract
Asarum sieboldii var. seoulense is a plant species under the family Aristolochiaceae and has been used for centuries as an ingredient in a well-known Traditional Chinese medicine (TCM), "Xixin", to treat symptoms of the neurodegenerative condition Parkinson's Disease (PD). Although there have been studies on the neuroprotective effect of this TCM, the phenotypic profiles of its chemical constituents against PD-implicated cellular organelles have not been reported. This research investigated the chemistry of A. sieboldii var. seoulense extract to identify the active small molecules that exhibited perturbation to the cellular compartments related to PD, potentially supporting its traditional application in treating this condition. 1H NMR-guided chemical investigation of this plant yielded twenty secondary metabolites which belong to isobutylamides, lignans and phenolics. The compounds were evaluated against an olfactory cell line derived from a PD patient using phenotypic assay. Several isolates, 2, 3, 7, 11, 13-16 and 18-20, were found to induce moderate perturbation to the staining of mitochondria, autophagosome and α-tubulin of the cells. Considering that PD pathogenesis is closely related to these cellular compartments, the results provided a rationale for the traditional application of Xixin in the treatment of PD.
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Affiliation(s)
- Chao Wang
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Thanh Nguyen
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Xinzhou Yang
- College of Pharmacy, South-Central University for Nationalities, Wuhan 430074, China
| | - George D Mellick
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia.
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10
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Tsunemoto H, Sugie J, Enustun E, Pogliano K, Pogliano J. Bacterial cytological profiling reveals interactions between jumbo phage φKZ infection and cell wall active antibiotics in Pseudomonas aeruginosa. PLoS One 2023; 18:e0280070. [PMID: 37418366 PMCID: PMC10328376 DOI: 10.1371/journal.pone.0280070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/20/2022] [Indexed: 07/09/2023] Open
Abstract
The emergence of antibiotic resistance in bacteria has led to the investigation of alternative treatments, such as phage therapy. In this study, we examined the interactions between the nucleus-forming jumbo phage ФKZ and antibiotic treatment against Pseudomonas aeruginosa. Using the fluorescence microscopy technique of bacterial cytological profiling, we identified mechanism-of-action-specific interactions between antibiotics that target different biosynthetic pathways and ФKZ infection. We found that certain classes of antibiotics strongly inhibited phage replication, while others had no effect or only mildly affected progression through the lytic cycle. Antibiotics that caused an increase in host cell length, such as the cell wall active antibiotic ceftazidime, prevented proper centering of the ФKZ nucleus via the PhuZ spindle at midcell, leading us to hypothesize that the kinetic parameters of the PhuZ spindle evolved to match the average length of the host cell. To test this, we developed a computational model explaining how the dynamic properties of the PhuZ spindle contribute to phage nucleus centering and why some antibiotics affect nucleus positioning while others do not. These findings provide an understanding of the molecular mechanisms underlying the interactions between antibiotics and jumbo phage replication.
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Affiliation(s)
- Hannah Tsunemoto
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Joseph Sugie
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Eray Enustun
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, United States of America
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11
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Herschede SR, Salam R, Gneid H, Busschaert N. Bacterial cytological profiling identifies transmembrane anion transport as the mechanism of action for a urea-based antibiotic. Supramol Chem 2023. [DOI: 10.1080/10610278.2023.2178921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- Sarah R. Herschede
- Department of Chemistry, Tulane University, New Orleans, Louisiana, United States
| | - Rayhanus Salam
- Department of Chemistry, Tulane University, New Orleans, Louisiana, United States
| | - Hassan Gneid
- Department of Chemistry, Tulane University, New Orleans, Louisiana, United States
| | - Nathalie Busschaert
- Department of Chemistry, Tulane University, New Orleans, Louisiana, United States
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12
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Abstract
As the global burden of antibiotic resistance continues to grow, creative approaches to antibiotic discovery are needed to accelerate the development of novel medicines. A rapidly progressing computational revolution-artificial intelligence-offers an optimistic path forward due to its ability to alleviate bottlenecks in the antibiotic discovery pipeline. In this review, we discuss how advancements in artificial intelligence are reinvigorating the adoption of past antibiotic discovery models-namely natural product exploration and small molecule screening. We then explore the application of contemporary machine learning approaches to emerging areas of antibiotic discovery, including antibacterial systems biology, drug combination development, antimicrobial peptide discovery, and mechanism of action prediction. Lastly, we propose a call to action for open access of high-quality screening datasets and interdisciplinary collaboration to accelerate the rate at which machine learning models can be trained and new antibiotic drugs can be developed.
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Affiliation(s)
- Telmah Lluka
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
| | - Jonathan M Stokes
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
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13
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Cylke KC, Si F, Banerjee S. Effects of antibiotics on bacterial cell morphology and their physiological origins. Biochem Soc Trans 2022; 50:1269-1279. [PMID: 36093840 PMCID: PMC10152891 DOI: 10.1042/bst20210894] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/05/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022]
Abstract
Characterizing the physiological response of bacterial cells to antibiotic treatment is crucial for the design of antibacterial therapies and for understanding the mechanisms of antibiotic resistance. While the effects of antibiotics are commonly characterized by their minimum inhibitory concentrations or the minimum bactericidal concentrations, the effects of antibiotics on cell morphology and physiology are less well characterized. Recent technological advances in single-cell studies of bacterial physiology have revealed how different antibiotic drugs affect the physiological state of the cell, including growth rate, cell size and shape, and macromolecular composition. Here, we review recent quantitative studies on bacterial physiology that characterize the effects of antibiotics on bacterial cell morphology and physiological parameters. In particular, we present quantitative data on how different antibiotic targets modulate cellular shape metrics including surface area, volume, surface-to-volume ratio, and the aspect ratio. Using recently developed quantitative models, we relate cell shape changes to alterations in the physiological state of the cell, characterized by changes in the rates of cell growth, protein synthesis and proteome composition. Our analysis suggests that antibiotics induce distinct morphological changes depending on their cellular targets, which may have important implications for the regulation of cellular fitness under stress.
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Affiliation(s)
- K. Callaghan Cylke
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Fangwei Si
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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14
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Antimicrobial and Cytotoxic Effects of Cannabinoids: An Updated Review with Future Perspectives and Current Challenges. Pharmaceuticals (Basel) 2022; 15:ph15101228. [PMID: 36297340 PMCID: PMC9607911 DOI: 10.3390/ph15101228] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
The development of new antibiotics is urgently needed to combat the threat of bacterial resistance. New classes of compounds that have novel properties are urgently needed for the development of effective antimicrobial agents. The extract of Cannabis sativa L. has been used to treat multiple ailments since ancient times. Its bioactivity is largely attributed to the cannabinoids found in its plant. Researchers are currently searching for new anti-infective agents that can treat various infections. Although its phytocannabinoid ingredients have a wide range of medical benefits beyond the treatment of infections, they are primarily associated to psychotropic effects. Different cannabinoids have been demonstrated to be helpful against harmful bacteria, including Gram-positive bacteria. Moreover, combination therapy involving the use of different antibiotics has shown synergism and broad-spectrum activity. The purpose of this review is to gather current data on the actions of Cannabis sativa (C. sativa) extracts and its primary constituents such as terpenes and cannabinoids towards pathogens in order to determine their antimicrobial properties and cytotoxic effects together with current challenges and future perspectives in biomedical application.
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15
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Miao WG, Nguyen T, Iqbal J, Pierens GK, Ma L, Richardson DR, Wood SA, Mellick GD, Quinn RJ, Feng Y. Meeting the Challenge 2: Identification of Potential Chemical Probes for Parkinson's Disease from Ligusticum chuanxiong Hort Using Cytological Profiling. ACS Chem Neurosci 2022; 13:2565-2578. [PMID: 36018577 DOI: 10.1021/acschemneuro.1c00820] [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: 01/20/2023] Open
Abstract
Traditional Chinese medicine (TCM) has been around for thousands of years and is increasingly gaining popularity in the Western world to treat various complex disorders including the incurable neurodegenerative condition, Parkinson's Disease (PD). One of the many directions in recent studies of PD is utilizing the phenotypic assay, or cytological profiling, to evaluate the phenotypic changes of PD-implicated cellular components in patient-derived olfactory neuroepithelial (hONS) cells, upon treating the cells with extracts or pure compounds. To obtain small molecules for studies utilizing PD phenotyping assays, Ligusticum chuanxiong Hort was selected for analysis as it is a popular Chinese herbal medicine used for treating PD-like symptoms. Fifty-three secondary metabolites, including six new compounds, were isolated from the ethanolic extract of L. chuanxiong; their structures were elucidated based on several spectroscopic techniques such as NMR, MS, Fourier transform infrared (FTIR), UV, and theoretical density functional theory (DFT) calculations. Cytological profiling of the afforded natural products against PD hONS cells revealed 34 compounds strongly perturbated the staining of several cellular organelles. In fact, greaterthan 1.5-fold change was observed compared to the control (dimethyl sulfoxide; DMSO), with early endosome, lysosome, and autophagosome (LC3b) being particularly affected. Given these biological compartments are closely related to PD pathogenesis, the results helped rationalize the traditional medicinal use of L. chuanxiong in PD treatment. Further, the hit compounds can serve as chemical probes to map the molecular pathways underlying PD, potentially leading to new therapeutic targets for PD.
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Affiliation(s)
- William Gang Miao
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Thanh Nguyen
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Jamila Iqbal
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Gregory K Pierens
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Linlin Ma
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Des R Richardson
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Stephen A Wood
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - George D Mellick
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia.,School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, 46 Don Young Road, Nathan, QLD 4111, Australia
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16
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Htoo HH, Tuyet NNT, Nakprasit K, Aonbangkhen C, Chaikeeratisak V, Chavasiri W, Nonejuie P. Mansonone G and its derivatives exhibit membrane permeabilizing activities against bacteria. PLoS One 2022; 17:e0273614. [PMID: 36048830 PMCID: PMC9436067 DOI: 10.1371/journal.pone.0273614] [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: 02/01/2022] [Accepted: 08/13/2022] [Indexed: 11/18/2022] Open
Abstract
In an era where the rate of bacteria evolving to be resistant to clinically-used antibiotics far exceeds that of antibiotic discovery, the search for new sources of antibacterial agents has expanded tremendously. In recent years, interest in plant-based natural products as promising sources of antibacterial agents has taken an upward trend. Mansonones, botanically-derived naphthoqionones, having many uses in Asian traditional medicine–including anti-infective roles–have sparked interest as a possible source of antibacterial agents. Here, we show that mansonone G, extracted from Mansonia gagei Drumm. heartwoods, possessed antibacterial activities towards Bacillus subtilis, Staphylococcus aureus and Escherichia coli lptD4213, inhibiting the growth of the bacteria at 15.6 μM, 62.5 μM and 125 μM, respectively. Fourteen derivatives of mansonone G were synthesized successfully and were found to have a similar antibacterial spectrum to that of the parent compound, with some derivatives possessing improved antibacterial activities. Bacterial cytological profiling analysis showed that mansonone G harbors membrane permeabilizing activities against B. subtilis and E. coli lptD4213. Temporal analysis of SYTOX Green staining among individual cells showed that mansonone G rapidly permeabilized bacterial membrane within 10 min, with SYTOX Green intensity reaching 13-fold above that of the control. Collectively, these findings highlight the importance of mansonone G and its derivatives as potential antibacterial agents, paving the way for further modifications in order to improve their antibacterial spectrum.
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Affiliation(s)
- Htut Htut Htoo
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Nhung Ngo Thi Tuyet
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Chulalongkorn University, Bangkok, Thailand
| | - Kittiporn Nakprasit
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Chulalongkorn University, Bangkok, Thailand
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Chulalongkorn University, Bangkok, Thailand
| | | | - Warinthorn Chavasiri
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Chulalongkorn University, Bangkok, Thailand
- * E-mail: (PN); (WC)
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
- * E-mail: (PN); (WC)
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17
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Haddad G, Takakura T, Bellali S, Fontanini A, Ominami Y, Khalil JB, Raoult D. A preliminary investigation into bacterial viability using scanning electron microscopy–energy-dispersive X-ray analysis: The case of antibiotics. Front Microbiol 2022; 13:967904. [PMID: 36003945 PMCID: PMC9393632 DOI: 10.3389/fmicb.2022.967904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
The metabolic stages of bacterial development and viability under different stress conditions induced by disinfection, chemical treatments, temperature, or atmospheric changes have been thoroughly investigated. Here, we aim to evaluate early metabolic modifications in bacteria following induced stress, resulting in alterations to bacterial metabolism. A protocol was optimized for bacterial preparation using energy-dispersive X-ray (EDX) microanalysis coupled with scanning electron microscopy (SEM), followed by optimizing EDX data acquisition and analysis. We investigated different preparation methods aiming to detect modifications in the bacterial chemical composition at different states. We first investigated Escherichia coli, acquiring data from fresh bacteria, after heat shock, and after contact with 70% ethanol, in order to prove the feasibility of this new strategy. We then applied the new method to different bacterial species following 1 h of incubation with increasing doses of antibiotics used as a stress-inducing agent. Among the different materials tested aiming to avoiding interaction with bacterial metabolites, phosphorous-doped silicon wafers were selected for the slide preparation. The 15 kV acceleration voltage ensured all the chemical elements of interest were excited. A thick layer of bacterial culture was deposited on the silicon wafer providing information from multiple cells and intra-cellular composition. The EDX spectra of fresh, heat-killed, and alcohol-killed E. coli revealed important modifications in magnesium, potassium, and sodium. Those same alterations were detected when applying this strategy to bacteria exposed to antibiotics. Tests based on SEM–EDX acquisition systems would provide early predictions of the bacterial viability state in different conditions, yielding earlier results than culture.
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Affiliation(s)
- Gabriel Haddad
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | | | - Sara Bellali
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Anthony Fontanini
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | | | - Jacques Bou Khalil
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Jacques Bou Khalil,
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- *Correspondence: Didier Raoult,
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18
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Montaño ET, Nideffer JF, Brumage L, Erb M, Busch J, Fernandez L, Derman AI, Davis JP, Estrada E, Fu S, Le D, Vuppala A, Tran C, Luterstein E, Lakkaraju S, Panchagnula S, Ren C, Doan J, Tran S, Soriano J, Fujita Y, Gutala P, Fujii Q, Lee M, Bui A, Villarreal C, Shing SR, Kim S, Freeman D, Racha V, Ho A, Kumar P, Falah K, Dawson T, Enustun E, Prichard A, Gomez A, Khanna K, Trigg S, Pogliano K, Pogliano J. Isolation and characterization of Streptomyces bacteriophages and Streptomyces strains encoding biosynthetic arsenals. PLoS One 2022; 17:e0262354. [PMID: 35061755 PMCID: PMC8782336 DOI: 10.1371/journal.pone.0262354] [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: 03/31/2021] [Accepted: 12/21/2021] [Indexed: 11/25/2022] Open
Abstract
The threat to public health posed by drug-resistant bacteria is rapidly increasing, as some of healthcare's most potent antibiotics are becoming obsolete. Approximately two-thirds of the world's antibiotics are derived from natural products produced by Streptomyces encoded biosynthetic gene clusters. Thus, to identify novel gene clusters, we sequenced the genomes of four bioactive Streptomyces strains isolated from the soil in San Diego County and used Bacterial Cytological Profiling adapted for agar plate culturing in order to examine the mechanisms of bacterial inhibition exhibited by these strains. In the four strains, we identified 104 biosynthetic gene clusters. Some of these clusters were predicted to produce previously studied antibiotics; however, the known mechanisms of these molecules could not fully account for the antibacterial activity exhibited by the strains, suggesting that novel clusters might encode antibiotics. When assessed for their ability to inhibit the growth of clinically isolated pathogens, three Streptomyces strains demonstrated activity against methicillin-resistant Staphylococcus aureus. Additionally, due to the utility of bacteriophages for genetically manipulating bacterial strains via transduction, we also isolated four new phages (BartholomewSD, IceWarrior, Shawty, and TrvxScott) against S. platensis. A genomic analysis of our phages revealed nearly 200 uncharacterized proteins, including a new site-specific serine integrase that could prove to be a useful genetic tool. Sequence analysis of the Streptomyces strains identified CRISPR-Cas systems and specific spacer sequences that allowed us to predict phage host ranges. Ultimately, this study identified Streptomyces strains with the potential to produce novel chemical matter as well as integrase-encoding phages that could potentially be used to manipulate these strains.
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Affiliation(s)
- Elizabeth T. Montaño
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jason F. Nideffer
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Lauren Brumage
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Marcella Erb
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Julia Busch
- Department of Immunology, Duke University, Durham, North Carolina, United Stated of America
| | - Lynley Fernandez
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alan I. Derman
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - John Paul Davis
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Elena Estrada
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sharon Fu
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Danielle Le
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Aishwarya Vuppala
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Cassidy Tran
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Elaine Luterstein
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Shivani Lakkaraju
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sriya Panchagnula
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Caroline Ren
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jennifer Doan
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sharon Tran
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Jamielyn Soriano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Yuya Fujita
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Pranathi Gutala
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Quinn Fujii
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Minda Lee
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Anthony Bui
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Carleen Villarreal
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Samuel R. Shing
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Sean Kim
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Danielle Freeman
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Vipula Racha
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Alicia Ho
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Prianka Kumar
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kian Falah
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Thomas Dawson
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Eray Enustun
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Amy Prichard
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Ana Gomez
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Shelly Trigg
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
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19
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Abstract
High-content imaging (HCI) is a technique for screening multiple cells in high resolution to detect subtle morphological and phenotypic variation. The method has been commonly deployed on model eukaryotic cellular systems, often for screening new drugs and targets. HCI is not commonly utilized for studying bacterial populations but may be a powerful tool in understanding and combatting antimicrobial resistance. Consequently, we developed a high-throughput method for phenotyping bacteria under antimicrobial exposure at the scale of individual bacterial cells. Imaging conditions were optimized on an Opera Phenix confocal microscope (Perkin Elmer), and novel analysis pipelines were established for both Gram-negative bacilli and Gram-positive cocci. The potential of this approach was illustrated using isolates of Klebsiella pneumoniae, Salmonella enterica serovar Typhimurium, and Staphylococcus aureus HCI enabled the detection and assessment of subtle morphological characteristics, undetectable through conventional phenotypical methods, that could reproducibly distinguish between bacteria exposed to different classes of antimicrobials with distinct modes of action (MOAs). In addition, distinctive responses were observed between susceptible and resistant isolates. By phenotyping single bacterial cells, we observed intrapopulation differences, which may be critical in identifying persistence or emerging resistance during antimicrobial treatment. The work presented here outlines a comprehensive method for investigating morphological changes at scale in bacterial populations under specific perturbation.IMPORTANCE High-content imaging (HCI) is a microscopy technique that permits the screening of multiple cells simultaneously in high resolution to detect subtle morphological and phenotypic variation. The power of this methodology is that it can generate large data sets comprised of multiple parameters taken from individual cells subjected to a range of different conditions. We aimed to develop novel methods for using HCI to study bacterial cells exposed to a range of different antibiotic classes. Using an Opera Phenix confocal microscope (Perkin Elmer) and novel analysis pipelines, we created a method to study the morphological characteristics of Klebsiella pneumoniae, Salmonella enterica serovar Typhimurium, and Staphylococcus aureus when exposed to antibacterial drugs with differing modes of action. By imaging individual bacterial cells at high resolution and scale, we observed intrapopulation differences associated with different antibiotics. The outlined methods are highly relevant for how we begin to better understand and combat antimicrobial resistance.
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20
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da Cunha BR, Zoio P, Fonseca LP, Calado CRC. Technologies for High-Throughput Identification of Antibiotic Mechanism of Action. Antibiotics (Basel) 2021; 10:565. [PMID: 34065815 PMCID: PMC8151116 DOI: 10.3390/antibiotics10050565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 01/23/2023] Open
Abstract
There are two main strategies for antibiotic discovery: target-based and phenotypic screening. The latter has been much more successful in delivering first-in-class antibiotics, despite the major bottleneck of delayed Mechanism-of-Action (MOA) identification. Although finding new antimicrobial compounds is a very challenging task, identifying their MOA has proven equally challenging. MOA identification is important because it is a great facilitator of lead optimization and improves the chances of commercialization. Moreover, the ability to rapidly detect MOA could enable a shift from an activity-based discovery paradigm towards a mechanism-based approach. This would allow to probe the grey chemical matter, an underexplored source of structural novelty. In this study we review techniques with throughput suitable to screen large libraries and sufficient sensitivity to distinguish MOA. In particular, the techniques used in chemical genetics (e.g., based on overexpression and knockout/knockdown collections), promoter-reporter libraries, transcriptomics (e.g., using microarrays and RNA sequencing), proteomics (e.g., either gel-based or gel-free techniques), metabolomics (e.g., resourcing to nuclear magnetic resonance or mass spectrometry techniques), bacterial cytological profiling, and vibrational spectroscopy (e.g., Fourier-transform infrared or Raman scattering spectroscopy) were discussed. Ultimately, new and reinvigorated phenotypic assays bring renewed hope in the discovery of a new generation of antibiotics.
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Affiliation(s)
- Bernardo Ribeiro da Cunha
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
| | - Paulo Zoio
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
- CIMOSM—Centro de Investigação em Modelação e Optimização de Sistemas Multifuncionais, ISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Luís P. Fonseca
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001 Lisboa, Portugal; (B.R.d.C.); (P.Z.); (L.P.F.)
| | - Cecília R. C. Calado
- CIMOSM—Centro de Investigação em Modelação e Optimização de Sistemas Multifuncionais, ISEL—Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
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21
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Ojkic N, Banerjee S. Bacterial cell shape control by nutrient-dependent synthesis of cell division inhibitors. Biophys J 2021; 120:2079-2084. [PMID: 33838134 DOI: 10.1016/j.bpj.2021.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/25/2021] [Accepted: 04/02/2021] [Indexed: 01/17/2023] Open
Abstract
By analyzing cell size and shapes of the bacterium Bacillus subtilis under nutrient perturbations, protein depletion, and antibiotic treatments, we find that cell geometry is extremely robust, reflected in a well-conserved scaling relation between surface area (S) and volume (V), S∼Vγ, with γ=0.85. We develop a molecular model supported by single-cell simulations to predict that the surface-to-volume scaling exponent γ is regulated by nutrient-dependent production of metabolic enzymes that act as cell division inhibitors in bacteria. Using theory that is supported by experimental data, we predict the modes of cell shape transformations in different bacterial species and propose a mechanism of cell shape adaptation to different nutrient perturbations. For organisms with high surface-to-volume scaling exponent γ, such as B. subtilis, cell width is not sensitive to growth-rate changes, whereas organisms with low γ, such as Acinetobacter baumannii, cell shape adapts readily to growth-rate changes.
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Affiliation(s)
- Nikola Ojkic
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania.
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22
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Chandrasekaran SN, Ceulemans H, Boyd JD, Carpenter AE. Image-based profiling for drug discovery: due for a machine-learning upgrade? Nat Rev Drug Discov 2021; 20:145-159. [PMID: 33353986 PMCID: PMC7754181 DOI: 10.1038/s41573-020-00117-w] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2020] [Indexed: 12/20/2022]
Abstract
Image-based profiling is a maturing strategy by which the rich information present in biological images is reduced to a multidimensional profile, a collection of extracted image-based features. These profiles can be mined for relevant patterns, revealing unexpected biological activity that is useful for many steps in the drug discovery process. Such applications include identifying disease-associated screenable phenotypes, understanding disease mechanisms and predicting a drug's activity, toxicity or mechanism of action. Several of these applications have been recently validated and have moved into production mode within academia and the pharmaceutical industry. Some of these have yielded disappointing results in practice but are now of renewed interest due to improved machine-learning strategies that better leverage image-based information. Although challenges remain, novel computational technologies such as deep learning and single-cell methods that better capture the biological information in images hold promise for accelerating drug discovery.
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Affiliation(s)
| | - Hugo Ceulemans
- Discovery Data Sciences, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Justin D Boyd
- High Content Imaging Technology Center, Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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23
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Blaskovich MAT, Kavanagh AM, Elliott AG, Zhang B, Ramu S, Amado M, Lowe GJ, Hinton AO, Pham DMT, Zuegg J, Beare N, Quach D, Sharp MD, Pogliano J, Rogers AP, Lyras D, Tan L, West NP, Crawford DW, Peterson ML, Callahan M, Thurn M. The antimicrobial potential of cannabidiol. Commun Biol 2021; 4:7. [PMID: 33469147 PMCID: PMC7815910 DOI: 10.1038/s42003-020-01530-y] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/20/2020] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial resistance threatens the viability of modern medicine, which is largely dependent on the successful prevention and treatment of bacterial infections. Unfortunately, there are few new therapeutics in the clinical pipeline, particularly for Gram-negative bacteria. We now present a detailed evaluation of the antimicrobial activity of cannabidiol, the main non-psychoactive component of cannabis. We confirm previous reports of Gram-positive activity and expand the breadth of pathogens tested, including highly resistant Staphylococcus aureus, Streptococcus pneumoniae, and Clostridioides difficile. Our results demonstrate that cannabidiol has excellent activity against biofilms, little propensity to induce resistance, and topical in vivo efficacy. Multiple mode-of-action studies point to membrane disruption as cannabidiol's primary mechanism. More importantly, we now report for the first time that cannabidiol can selectively kill a subset of Gram-negative bacteria that includes the 'urgent threat' pathogen Neisseria gonorrhoeae. Structure-activity relationship studies demonstrate the potential to advance cannabidiol analogs as a much-needed new class of antibiotics.
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Affiliation(s)
- Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Angela M Kavanagh
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Alysha G Elliott
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Bing Zhang
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Soumya Ramu
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Maite Amado
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Gabrielle J Lowe
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Alexandra O Hinton
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Do Minh Thu Pham
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Johannes Zuegg
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Neil Beare
- BDG Synthesis, Wellington, 5045, New Zealand
| | - Diana Quach
- Linnaeus Bioscience Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Marc D Sharp
- Linnaeus Bioscience Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Joe Pogliano
- Linnaeus Bioscience Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
- Division of Biological Sciences, University of California, San Diego, CA, 92093, USA
| | - Ashleigh P Rogers
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, 3800, Australia
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, 3800, Australia
| | - Lendl Tan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Nicholas P West
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - David W Crawford
- Perfectus Biomed, LLC (formerly Extherid Biosciences), 3545 S Park Dr, Jackson, WY, 83001, USA
| | - Marnie L Peterson
- Perfectus Biomed, LLC (formerly Extherid Biosciences), 3545 S Park Dr, Jackson, WY, 83001, USA
| | - Matthew Callahan
- Botanix Pharmaceuticals Ltd., Level 1, 50 Angove Street, North Perth, WA, 6005, Australia
| | - Michael Thurn
- Botanix Pharmaceuticals Ltd., Level 1, 50 Angove Street, North Perth, WA, 6005, Australia
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24
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Rajput A, Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Seif Y, Lamsa A, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Knight R, Pogliano J, Nizet V, Feist AM, Palsson BO. Identifying the effect of vancomycin on health care-associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media. Gigascience 2021; 10:6072295. [PMID: 33420779 PMCID: PMC7794652 DOI: 10.1093/gigascience/giaa156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The evolving antibiotic-resistant behavior of health care-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) USA100 strains are of major concern. They are resistant to a broad class of antibiotics such as macrolides, aminoglycosides, fluoroquinolones, and many more. FINDINGS The selection of appropriate antibiotic susceptibility examination media is very important. Thus, we use bacteriological (cation-adjusted Mueller-Hinton broth) as well as physiological (R10LB) media to determine the effect of vancomycin on USA100 strains. The study includes the profiling behavior of HA-MRSA USA100 D592 and D712 strains in the presence of vancomycin through various high-throughput assays. The US100 D592 and D712 strains were characterized at sub-inhibitory concentrations through growth curves, RNA sequencing, bacterial cytological profiling, and exo-metabolomics high throughput experiments. CONCLUSIONS The study reveals the vancomycin resistance behavior of HA-MRSA USA100 strains in dual media conditions using wide-ranging experiments.
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Affiliation(s)
- Akanksha Rajput
- Department of Bioengineering, University of California, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Saugat Poudel
- Department of Bioengineering, University of California, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Hannah Tsunemoto
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Michael Meehan
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Connor A Olson
- Department of Bioengineering, University of California, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Yara Seif
- Department of Bioengineering, University of California, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Anne Lamsa
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Nicholas Dillon
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92023, USA.,Collaborative to Halt Antibiotic-Resistant Microbes (CHARM), Department of Pediatrics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Alison Vrbanac
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92023, USA.,Collaborative to Halt Antibiotic-Resistant Microbes (CHARM), Department of Pediatrics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Joseph Sugie
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Samira Dahesh
- Department of Pediatrics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92023, USA.,Collaborative to Halt Antibiotic-Resistant Microbes (CHARM), Department of Pediatrics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Jonathan M Monk
- Department of Bioengineering, University of California, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Center for Microbiome Innovation, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Rob Knight
- Department of Bioengineering, University of California, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92023, USA.,Center for Microbiome Innovation, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Victor Nizet
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92023, USA.,Collaborative to Halt Antibiotic-Resistant Microbes (CHARM), Department of Pediatrics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Center for Microbiome Innovation, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA
| | - Adam M Feist
- Department of Bioengineering, University of California, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92023, USA.,Center for Microbiome Innovation, University of California San Diego, 9500 Gilman Dr, La Jolla, CA 92093, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens, Lyngby, Denmark
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25
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Schäfer AB, Wenzel M. A How-To Guide for Mode of Action Analysis of Antimicrobial Peptides. Front Cell Infect Microbiol 2020; 10:540898. [PMID: 33194788 PMCID: PMC7604286 DOI: 10.3389/fcimb.2020.540898] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
Antimicrobial peptides (AMPs) are a promising alternative to classical antibiotics in the fight against multi-resistant bacteria. They are produced by organisms from all domains of life and constitute a nearly universal defense mechanism against infectious agents. No drug can be approved without information about its mechanism of action. In order to use them in a clinical setting, it is pivotal to understand how AMPs work. While many pore-forming AMPs are well-characterized in model membrane systems, non-pore-forming peptides are often poorly understood. Moreover, there is evidence that pore formation may not happen or not play a role in vivo. It is therefore imperative to study how AMPs interact with their targets in vivo and consequently kill microorganisms. This has been difficult in the past, since established methods did not provide much mechanistic detail. Especially, methods to study membrane-active compounds have been scarce. Recent advances, in particular in microscopy technology and cell biological labeling techniques, now allow studying mechanisms of AMPs in unprecedented detail. This review gives an overview of available in vivo methods to investigate the antibacterial mechanisms of AMPs. In addition to classical mode of action classification assays, we discuss global profiling techniques, such as genomic and proteomic approaches, as well as bacterial cytological profiling and other cell biological assays. We cover approaches to determine the effects of AMPs on cell morphology, outer membrane, cell wall, and inner membrane properties, cellular macromolecules, and protein targets. We particularly expand on methods to examine cytoplasmic membrane parameters, such as composition, thickness, organization, fluidity, potential, and the functionality of membrane-associated processes. This review aims to provide a guide for researchers, who seek a broad overview of the available methodology to study the mechanisms of AMPs in living bacteria.
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Affiliation(s)
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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26
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Lucidi M, Hristu R, Nichele L, Stanciu GA, Tranca DE, Holban AM, Visca P, Stanciu SG, Cincotti G. STED nanoscopy of KK114-stained pathogenic bacteria. JOURNAL OF BIOPHOTONICS 2020; 13:e202000097. [PMID: 32483852 DOI: 10.1002/jbio.202000097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/11/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Super-resolution microscopy techniques can provide answers to still pending questions on prokaryotic organisms but are yet to be used at their full potential for this purpose. To address this, we evaluate the ability of the rhodamine-like KK114 dye to label various types of bacteria, to enable imaging of fine structural details with stimulated emission depletion microscopy (STED). We assessed fluorescent labeling with KK114 for eleven Gram-positive and Gram-negative bacterial species and observed that this contrast agent binds to their cell membranes. Significant differences in the labeling outputs were noticed across the tested bacterial species, but importantly, KK114-staining allowed the observation of subtle nanometric cell details in some cases. For example, a helix pattern resembling a cytoskeleton arrangement was detected in Bacillus subtilis. Furthermore, we found that KK114 easily penetrates the membrane of bacterial microorganism that lost their viability, which can be useful to discriminate between living and dead cells.
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Affiliation(s)
| | - Radu Hristu
- Center for Microscopy - Microanalysis and Information Processing, University Politehnica of Bucharest, Bucharest, Romania
| | | | - George A Stanciu
- Center for Microscopy - Microanalysis and Information Processing, University Politehnica of Bucharest, Bucharest, Romania
| | - Denis E Tranca
- Center for Microscopy - Microanalysis and Information Processing, University Politehnica of Bucharest, Bucharest, Romania
| | - Alina Maria Holban
- Microbiology and Immunology Department, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Paolo Visca
- Department of Sciences, University Roma Tre, Rome, Italy
| | - Stefan G Stanciu
- Center for Microscopy - Microanalysis and Information Processing, University Politehnica of Bucharest, Bucharest, Romania
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27
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Nguyen DT, Iqbal J, Han J, Pierens GK, Wood SA, Mellick GD, Feng Y. Chemical constituents from Macleaya cordata (Willd) R. Br. and their phenotypic functions against a Parkinson's disease patient-derived cell line. Bioorg Med Chem 2020; 28:115732. [PMID: 33065438 DOI: 10.1016/j.bmc.2020.115732] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/02/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022]
Abstract
Cytological profiling (CP) assay against a human olfactory neuroshpere-derived (hONS) cell line using a library of traditional Chinese medicinal plant extracts gave indications that the ethanolic extract of Macleaya cordata (Willd) R. Br. elicited strong perturbations to various cellular components. Further chemical investigation of this extract resulted in the isolation of two new benzo[c]phenanthridine alkaloids, (6R)-10-methoxybocconoline (1) and 6-(1-hydroxyethyl)-10-methoxy-5,6-dihydrochelerythrine (2). Their planar structures were elucidated by extensive 1D and 2D NMR studies, together with MS data. The absolute configuration for position C-6 of 1 and relative configurations for position C-6 and C-1' of 2 were assigned by density functional theory (DFT) calculations of ECD and NMR data, respectively. Also isolated were fourteen known metabolites, including ten alkaloids (3-12) and four coumaroyl-containing compounds (13-16). Cytological profiling of the isolates against Parkinson's Disease (PD) patient-derived olfactory cells revealed bocconoline (3) and 6-(1-hydroxyethyl)-5,6-dihydrochelerythrine (4) significantly perturbated the features of cellular organelles including early endosomes, mitochondria and autophagosomes. Given that hONS cells from PD patients model some functional aspects of the disease, the results suggested that these phenotypic profiles may have a role in the mechanisms underlying PD and signified the efficacy of CP in finding potential chemical tools to study the biological pathways in PD.
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Affiliation(s)
- Duy Thanh Nguyen
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Jamila Iqbal
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Jianying Han
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Gregory K Pierens
- Centre for Advanced Imaging, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Stephen A Wood
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - George D Mellick
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia.
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28
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Yoon J, Kim Y, Suh JW, Jin YY, Jung YG, Park W. Bacterial Isolation Microwell-Plug (μWELLplug) for Rapid Antibiotic Susceptibility Testing Using Morphology Analysis. ACS APPLIED BIO MATERIALS 2020; 3:4798-4808. [PMID: 35021726 DOI: 10.1021/acsabm.0c00317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The rapid and accurate diagnosis of infectious diseases with high morbidity rates is crucial because it can minimize the misuse and overuse of antibiotics and increase survival rates in dreadful conditions. The conventional antibiotic susceptibility test (AST) systems used to choose appropriate antibiotics require long wait times to obtain results and cannot prevent the misuse or overuse of antibiotics by clinicians who need to quickly treat patients and cannot wait to identify the underlying cause of their symptoms. Therefore, several rapid AST (rAST) methods have been developed to provide quick test results, but they are complicated to operate, require additional equipment or materials, and give less accurate results than the conventional AST methods. In this study, we propose an rAST method that can obtain precise outcomes from a simple process with a short running time using a bacterial isolation microwell-plug (μWELLplug) in a conventional 96-well plate. The specifically designed hydrogel component of the μWELLplug provides a simple process for cell isolation and the observation of bacterial growth and morphological changes induced by a variety of antibiotic concentrations. The μWELLplug is placed over each well of the 96-well plate, and then bacterial or eukaryotic cells are isolated in the microwells and treated with different antibiotic concentrations to observe their effects. Saccharomyces cerevisiae (yeast, eukaryote), Streptomyces atratus (actinomycetes, prokaryote), Escherichia coli, Staphylococcus aureus, and methicillin-resistant S. aureus were cultivated and tested using the μWELLplug. The minimum inhibitory concentration values from this system were obtained in 3-4 h and correlated well with those from the conventional AST methods whose running time is 18-24 h.
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Affiliation(s)
- Jinsik Yoon
- Department of Electronic Engineering, Kyung Hee University, Yongin-si 17104, Republic of Korea
| | - Youngkyoung Kim
- Graduate School of Interdisciplinary Program of Biomodulation, Myongji University, Yongin 17058, Gyeonggi-do, Republic of Korea
| | - Joo-Won Suh
- Graduate School of Interdisciplinary Program of Biomodulation, Myongji University, Yongin 17058, Gyeonggi-do, Republic of Korea.,Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin 17058, Gyeonggi-do, Republic of Korea
| | - Ying-Yu Jin
- Graduate School of Interdisciplinary Program of Biomodulation, Myongji University, Yongin 17058, Gyeonggi-do, Republic of Korea
| | - Yong-Gyun Jung
- Graduate School of Interdisciplinary Program of Biomodulation, Myongji University, Yongin 17058, Gyeonggi-do, Republic of Korea.,Ezdiatech Inc., Anyang-si 14058, Gyeonggi-do, Republic of Korea
| | - Wook Park
- Department of Electronic Engineering, Kyung Hee University, Yongin-si 17104, Republic of Korea
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29
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Schulte AJ, Agan BK, Wang HC, McGann PT, Davies BW, Legault GL, Justin GA. Multidrug-Resistant Organisms from Ophthalmic Cultures: Antibiotic Resistance and Visual Acuity. Mil Med 2020; 185:e1002-e1007. [PMID: 32588895 DOI: 10.1093/milmed/usaa111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
INTRODUCTION There is a growing trend of multidrug-resistant organisms (MDRO). The goal of this study was to characterize MDRO at a single center from ophthalmic cultures to better understand how treatments were tailored and to assess effect on visual acuity. MATERIALS AND METHODS The MDRO data were collected by the Multidrug-Resistant Organism Repository and Surveillance Network from the Brooke Army Medical Center clinical laboratory. Both patient- and isolate-specific data were collected and qualitatively analyzed. Primary outcome measures were organism and type of resistance, anatomic location of isolate, initial and final antibiotic choice, and visual acuity. RESULTS Thirty-one bacterial culture samples were analyzed from 29 patients. Twenty-two (72%) were Gram-positive and all were methicillin-resistant Staphylococcus aureus (MRSA). Nine (29%) were Gram-negative and of these five were Pseudomonas spp. Fourteen (45%) isolates were cultured from the cornea, nine (29%) from the lid, four (13%) from the conjunctiva, and four (13%) from other locations. The majority (66.6%) required adjustment of initial antibiotics following ocular culture results. Sixteen adult patients had recorded initial and final visual acuities. Fifteen of those 16 patients had stable or improved visual acuities following treatment of the infection, but five patients had a final visual acuity less than 20/200. CONCLUSION This study demonstrated a high frequency of corneal MDRO infections and specifically MRSA and Pseudomonas spp. isolates. Antibiotic treatments frequently required adjustment. Further prospective study of visual outcomes from ophthalmic MDRO cultures is needed.
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Affiliation(s)
- Alexandra J Schulte
- Department of Ophthalmology, Brooke Army Medical Center, 3551 Roger Brooke Drive, San Antonio, TX 78234
| | - Brian K Agan
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814.,Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Dr, Bethesda, MD 20817
| | - Heuy-Ching Wang
- Naval Medical Research Unit, Combat Casualty Care and Operational Medicine, 2330 Stanley Rd, San Antonio, TX 78234
| | - Patrick T McGann
- Department of Molecular Research, 503 Robert Grant Ave, 20910, Multidrug Resistant Organism Repository and Surveillance Network, Silver Spring, MD
| | - Brett W Davies
- Department of Surgery, Uniformed Services University of the Health Science, 4301 Jones Bridge Road, 20814 Bethesda, MD.,Department of Ophthalmology, Wilford Hall Eye Center, 1100 Wilford Hall Loop, 78236 San Antonio, TX
| | - Gary L Legault
- Department of Ophthalmology, Brooke Army Medical Center, 3551 Roger Brooke Drive, San Antonio, TX 78234.,Department of Surgery, Uniformed Services University of the Health Science, 4301 Jones Bridge Road, 20814 Bethesda, MD
| | - Grant A Justin
- Department of Ophthalmology, Brooke Army Medical Center, 3551 Roger Brooke Drive, San Antonio, TX 78234.,Department of Surgery, Uniformed Services University of the Health Science, 4301 Jones Bridge Road, 20814 Bethesda, MD
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30
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Ersoy SC, Otmishi M, Milan VT, Li L, Pak Y, Mediavilla J, Chen L, Kreiswirth B, Chambers HF, Proctor RA, Xiong YQ, Fowler VG, Bayer AS. Scope and Predictive Genetic/Phenotypic Signatures of Bicarbonate (NaHCO 3) Responsiveness and β-Lactam Sensitization in Methicillin-Resistant Staphylococcus aureus. Antimicrob Agents Chemother 2020; 64:e02445-19. [PMID: 32041719 PMCID: PMC7179597 DOI: 10.1128/aac.02445-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
Addition of sodium bicarbonate (NaHCO3) to standard antimicrobial susceptibility testing medium reveals certain methicillin-resistant Staphylococcus aureus (MRSA) strains to be highly susceptible to β-lactams. We investigated the prevalence of this phenotype (NaHCO3 responsiveness) to two β-lactams among 58 clinical MRSA bloodstream isolates. Of note, ∼75% and ∼36% of isolates displayed the NaHCO3 responsiveness phenotype to cefazolin (CFZ) and oxacillin (OXA), respectively. Neither intrinsic β-lactam MICs in standard Mueller-Hinton broth (MHB) nor population analysis profiles were predictive of this phenotype. Several genotypic markers (clonal complex 8 [CC8]; agr I and spa t008) were associated with NaHCO3 responsiveness for OXA.
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Affiliation(s)
| | - Mariam Otmishi
- California State University Dominguez Hills, Carson, California, USA
| | | | - Liang Li
- The Lundquist Institute, Torrance, California, USA
| | - Youngju Pak
- The Lundquist Institute, Torrance, California, USA
| | | | - Liang Chen
- Meridian Health, Nutley, New Jersey, USA
| | | | | | - Richard A Proctor
- University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Yan Q Xiong
- The Lundquist Institute, Torrance, California, USA
- Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Vance G Fowler
- Duke University Medical Center, School of Medicine, Durham, North Carolina, USA
| | - Arnold S Bayer
- The Lundquist Institute, Torrance, California, USA
- Geffen School of Medicine at UCLA, Los Angeles, California, USA
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31
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Monitoring of drug resistance towards reducing the toxicity of pharmaceutical compounds: Past, present and future. J Pharm Biomed Anal 2020; 186:113265. [PMID: 32283481 DOI: 10.1016/j.jpba.2020.113265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/15/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022]
Abstract
Drug resistance is worldwide health care crisis which decrease drug efficacy and developing toxicities. Effective resistance detection techniques could alleviate treatment cost and mortality associated with this crisis. In this review, the conventional and modern analysis methods for monitoring of drug resistance are presented. Also, various types of emerging rapid and sensitive techniques including electrochemical, electrical, optical and nano-based methods for the screening of drug resistance were discussed. Applications of various methods for the sensitive and rapid detection of drug resistance are investigated. The review outlines existing key issues in the determination which must be overcome before any of these techniques becomes a feasible method for the rapid detection of drug resistance. In this review, the roles of nanomaterials on development of novel methods for the monitoring of drug resistance were presented. Also, limitations and challenges of conventional and modern methods were discussed.
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32
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Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media. Sci Data 2019; 6:322. [PMID: 31848353 PMCID: PMC6917727 DOI: 10.1038/s41597-019-0331-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/07/2019] [Indexed: 01/05/2023] Open
Abstract
Staphylococcus aureus strains have been continuously evolving resistance to numerous classes of antibiotics including methicillin, vancomycin, daptomycin and linezolid, compounding the enormous healthcare and economic burden of the pathogen. Cation-adjusted Mueller-Hinton broth (CA-MHB) is the standard bacteriological media for measuring antibiotic susceptibility in the clinical lab, but the use of media that more closely mimic the physiological state of the patient, e.g. mammalian tissue culture media, can in certain circumstances reveal antibiotic activities that may be more predictive of effectiveness in vivo. In the current study, we use both types of media to explore antibiotic resistance phenomena in hospital-acquired USA100 lineage methicillin-resistant, vancomycin-intermediate Staphylococcus aureus (MRSA/VISA) strain D712 via multidimensional high throughput analysis of growth rates, bacterial cytological profiling, RNA sequencing, and exo-metabolomics (HPLC and LC-MS). Here, we share data generated from these assays to shed light on the antibiotic resistance behavior of MRSA/VISA D712 in both bacteriological and physiological media. Measurement(s) | Antibacterial Response • cDNA • transcription profiling assay • culture medium • organic acid | Technology Type(s) | bacterial cytological profiling • RNA sequencing • liquid chromatography-tandem mass spectrometry • high-performance liquid chromatography | Factor Type(s) | growth medium | Sample Characteristic - Organism | Staphylococcus aureus |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.10283108
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An active domain HF-18 derived from hagfish intestinal peptide effectively inhibited drug-resistant bacteria in vitro/vivo. Biochem Pharmacol 2019; 172:113746. [PMID: 31812678 DOI: 10.1016/j.bcp.2019.113746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/03/2019] [Indexed: 01/03/2023]
Abstract
Antibiotic resistance is spreading faster than the development of new antibiotics into clinical practice. Currently, the design of antimicrobial peptides (AMPs), potential new antibacterial agents with rare antimicrobial resistance, is the available strategy to enhance the antimicrobial activity and lower the toxicity of AMPs. In this study, a peptide derived from hagfish intestinal peptide was designed and termed as HF-18 (GFFKKAWRKVKKAFRRVL). After antimicrobial/bactericidal test in vitro, we found that HF-18 exhibited a potent antimicrobial activity with MIC of only 4 μg/ml against drug-resistant Staphylococcus aureus (S. aureus). Meanwhile, it eliminated the test bacteria within 1 h, suggesting its rapid bactericidal effect. Importantly, this peptide had no obvious hemolytic activity and cytotoxicity to mammalian cells. Furthermore, its notable antimicrobial effects in vivo was confirmed again in S. aureus induced mouse bacteremia and skin wound infection, reflecting as the decrease in bacterial counts in mouse lung or skin (up to 1.9 or 3.5 log CFU respectively), and including the inhibitory activity on inflammatory cytokines secretion. The possible mechanisms underlying HF-18 against drug-resistant S. aureus may attribute that HF-18 neutralized the negative charge in S. aureus surface and then disrupted the integrity of cell membranes to enhance the permeation of bacterial membrane, showing as the increased uptake of NPN and PI and the obvious morphology changes of S. aureus. In addition, this peptide bound to bacterial genomic DNA to suppress the expression of Panton-Valentine leukocidin (pvl) and nuclease (nuc) genes, which play major roles in S. aureus virulence. The properties of HF-18 suggest a path towards developing antibacterial agents that has stronger antibacterial activity and greater security for clinical treatment of infection induced by S. aureus, especially drug-resistant S. aureus.
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Bhattacharyya RP, Bandyopadhyay N, Ma P, Son SS, Liu J, He LL, Wu L, Khafizov R, Boykin R, Cerqueira GC, Pironti A, Rudy RF, Patel MM, Yang R, Skerry J, Nazarian E, Musser KA, Taylor J, Pierce VM, Earl AM, Cosimi LA, Shoresh N, Beechem J, Livny J, Hung DT. Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination. Nat Med 2019; 25:1858-1864. [PMID: 31768064 PMCID: PMC6930013 DOI: 10.1038/s41591-019-0650-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/11/2019] [Indexed: 12/13/2022]
Abstract
Multidrug resistant organisms (MDROs) are a serious threat to human health1,2. Fast, accurate antibiotic susceptibility testing (AST) is a critical need in addressing escalating antibiotic resistance, since delays in identifying MDROs increase mortality3,4 and use of broad-spectrum antibiotics, further selecting for resistant organisms. Yet current growth-based AST assays, such as broth microdilution5, require several days before informing key clinical decisions. Rapid AST would transform the care of infected patients while ensuring that our antibiotic arsenal is deployed as efficiently as possible. Growth-based assays are fundamentally constrained in speed by doubling time of the pathogen, and genotypic assays are limited by the ever-growing diversity and complexity of bacterial antibiotic resistance mechanisms. Here, we describe a rapid assay for combined Genotypic and Phenotypic AST through RNA detection, GoPhAST-R, that classifies strains with 94–99% accuracy by coupling machine learning analysis of early antibiotic-induced transcriptional changes with simultaneous detection of key genetic resistance determinants to increase accuracy of resistance detection, facilitate molecular epidemiology, and enable early detection of emerging resistance mechanisms. This two-pronged approach provides phenotypic AST 24–36 hours faster than standard workflows, with <4 hour assay time on a pilot instrument for hybridization-based multiplexed RNA detection implemented directly from positive blood cultures.
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Affiliation(s)
- Roby P Bhattacharyya
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nirmalya Bandyopadhyay
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Peijun Ma
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sophie S Son
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jamin Liu
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lorrie L He
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lidan Wu
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Rich Boykin
- NanoString Technologies, Inc., Seattle, WA, USA
| | - Gustavo C Cerqueira
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Personal Genome Diagnostics, Ellicott City, MD, USA
| | - Alejandro Pironti
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Robert F Rudy
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Milesh M Patel
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Rui Yang
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jennifer Skerry
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kimberly A Musser
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jill Taylor
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Virginia M Pierce
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lisa A Cosimi
- Infectious Diseases Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Noam Shoresh
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Deborah T Hung
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
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Ojkic N, Serbanescu D, Banerjee S. Surface-to-volume scaling and aspect ratio preservation in rod-shaped bacteria. eLife 2019; 8:e47033. [PMID: 31456563 PMCID: PMC6742476 DOI: 10.7554/elife.47033] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/28/2019] [Indexed: 01/16/2023] Open
Abstract
Rod-shaped bacterial cells can readily adapt their lengths and widths in response to environmental changes. While many recent studies have focused on the mechanisms underlying bacterial cell size control, it remains largely unknown how the coupling between cell length and width results in robust control of rod-like bacterial shapes. In this study we uncover a conserved surface-to-volume scaling relation in Escherichia coli and other rod-shaped bacteria, resulting from the preservation of cell aspect ratio. To explain the mechanistic origin of aspect-ratio control, we propose a quantitative model for the coupling between bacterial cell elongation and the accumulation of an essential division protein, FtsZ. This model reveals a mechanism for why bacterial aspect ratio is independent of cell size and growth conditions, and predicts cell morphological changes in response to nutrient perturbations, antibiotics, MreB or FtsZ depletion, in quantitative agreement with experimental data.
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Affiliation(s)
- Nikola Ojkic
- Department of Physics and Astronomy, Institute for the Physics of Living SystemsUniversity College LondonLondonUnited Kingdom
| | - Diana Serbanescu
- Department of Physics and Astronomy, Institute for the Physics of Living SystemsUniversity College LondonLondonUnited Kingdom
| | - Shiladitya Banerjee
- Department of Physics and Astronomy, Institute for the Physics of Living SystemsUniversity College LondonLondonUnited Kingdom
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Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, Nizet V, Palsson BO, Feist AM. Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media. Sci Data 2019; 6:43. [PMID: 31028276 PMCID: PMC6486602 DOI: 10.1038/s41597-019-0051-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/07/2019] [Indexed: 12/05/2022] Open
Abstract
Cation adjusted-Mueller Hinton Broth (CA-MHB) is the standard bacteriological medium utilized in the clinic for the determination of antibiotic susceptibility. However, a growing number of literature has demonstrated that media conditions can cause a substantial difference in the efficacy of antibiotics and antimicrobials. Recent studies have also shown that minimum inhibitory concentration (MIC) tests performed in standard cell culture media (e.g. RPMI and DMEM) are more indicative of in vivo antibiotic efficacy, presumably because they are a better proxy for the human host’s physiological conditions. The basis for the bacterial media dependent susceptibility to antibiotics remains undefined. To address this question, we characterized the physiological response of methicillin-resistant Staphylococcus aureus (MRSA) during exposure to sub-inhibitory concentrations of the beta-lactam antibiotic nafcillin in either CA-MHB or RPMI + 10% LB (R10LB). Here, we present high quality transcriptomic, exo-metabolomic and morphological data paired with growth and susceptibility results for MRSA cultured in either standard bacteriologic or more physiologic relevant medium. Design Type(s) | replicate design • transcription profiling design • sequence analysis objective | Measurement Type(s) | transcription profiling assay • cellular morphology • exo-metabolome • growth | Technology Type(s) | RNA sequencing • fluorescence microscopy • liquid chromatography-tandem mass spectrometry • high performance liquid chromatography • Optical Density Measurement | Factor Type(s) | culture medium • biological replicate • experimental condition | Sample Characteristic(s) | Staphylococcus aureus • culturing environment |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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Affiliation(s)
- Saugat Poudel
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Hannah Tsunemoto
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Michael Meehan
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Connor A Olson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Anne Lamsa
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yara Seif
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Nicholas Dillon
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Alison Vrbanac
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Joseph Sugie
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Samira Dahesh
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, California, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
| | - Joseph Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, USA.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, 92093, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
| | - Victor Nizet
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, USA.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kongens, Lyngby, Denmark.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, 92093, USA
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, USA. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kongens, Lyngby, Denmark.
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Bacterial Cytological Profiling as a Tool To Study Mechanisms of Action of Antibiotics That Are Active against Acinetobacter baumannii. Antimicrob Agents Chemother 2019; 63:AAC.02310-18. [PMID: 30745382 DOI: 10.1128/aac.02310-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/30/2019] [Indexed: 01/09/2023] Open
Abstract
An increasing number of multidrug-resistant Acinetobacter baumannii (MDR-AB) infections have been reported worldwide, posing a threat to public health. The establishment of methods to elucidate the mechanism of action (MOA) of A. baumannii-specific antibiotics is needed to develop novel antimicrobial therapeutics with activity against MDR-AB We previously developed bacterial cytological profiling (BCP) to understand the MOA of compounds in Escherichia coli and Bacillus subtilis Given how distantly related A. baumannii is to these species, it was unclear to what extent it could be applied. Here, we implemented BCP as an antibiotic MOA discovery platform for A. baumannii We found that the BCP platform can distinguish among six major antibiotic classes and can also subclassify antibiotics that inhibit the same cellular pathway but have different molecular targets. We used BCP to show that the compound NSC145612 inhibits the growth of A. baumannii via targeting RNA transcription. We confirmed this result by isolating and characterizing resistant mutants with mutations in the rpoB gene. Altogether, we conclude that BCP provides a useful tool for MOA studies of antibacterial compounds that are active against A. baumannii.
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Maugeri G, Lychko I, Sobral R, Roque ACA. Identification and Antibiotic-Susceptibility Profiling of Infectious Bacterial Agents: A Review of Current and Future Trends. Biotechnol J 2019; 14:e1700750. [PMID: 30024110 PMCID: PMC6330097 DOI: 10.1002/biot.201700750] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/06/2018] [Indexed: 12/16/2022]
Abstract
Antimicrobial resistance is one of the most worrying threats to humankind with extremely high healthcare costs associated. The current technologies used in clinical microbiology to identify the bacterial agent and profile antimicrobial susceptibility are time-consuming and frequently expensive. As a result, physicians prescribe empirical antimicrobial therapies. This scenario is often the cause of therapeutic failures, causing higher mortality rates and healthcare costs, as well as the emergence and spread of antibiotic resistant bacteria. As such, new technologies for rapid identification of the pathogen and antimicrobial susceptibility testing are needed. This review summarizes the current technologies, and the promising emerging and future alternatives for the identification and profiling of antimicrobial resistance bacterial agents, which are expected to revolutionize the field of clinical diagnostics.
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Affiliation(s)
- Gaetano Maugeri
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Iana Lychko
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Rita Sobral
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
| | - Ana C A Roque
- UCIBIO, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2819-516, Caparica, Portugal
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Peters CE, Lamsa A, Liu RB, Quach D, Sugie J, Brumage L, Pogliano J, Lopez-Garrido J, Pogliano K. Rapid Inhibition Profiling Identifies a Keystone Target in the Nucleotide Biosynthesis Pathway. ACS Chem Biol 2018; 13:3251-3258. [PMID: 30133247 DOI: 10.1021/acschembio.8b00273] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Understanding the mechanism of action (MOA) of new antimicrobial agents is a critical step in drug discovery but is notoriously difficult for compounds that appear to inhibit multiple cellular pathways. We recently described image-based approaches [bacterial cytological profiling and rapid inducible profiling (RIP)] for identifying the cellular pathways targeted by antibiotics. Here we have applied these methods to examine the effects of proteolytically degrading enzymes involved in pyrimidine nucleotide biosynthesis, a pathway that produces intermediates for transcription, DNA replication, and cell envelope synthesis. We show that rapid removal of enzymes directly involved in deoxyribonucleotide synthesis blocks DNA replication. However, degradation of cytidylate kinase (CMK), which catalyzes reactions involved in the synthesis of both ribonucleotides and deoxyribonucleotides, blocks both DNA replication and wall teichoic acid biosynthesis, producing cytological effects identical to those created by simultaneously inhibiting both processes with the antibiotics ciprofloxacin and tunicamycin. Our results suggest that RIP can be used to identify and characterize potential keystone enzymes like CMK whose inhibition dramatically affects multiple pathways, thereby revealing important metabolic connections. Identifying and understanding the role of keystone targets might also help to determine the MOAs of drugs that appear to inhibit multiple targets.
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Affiliation(s)
- Christine E. Peters
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Anne Lamsa
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Roland B. Liu
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Diana Quach
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Joseph Sugie
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Lauren Brumage
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Javier Lopez-Garrido
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California 92093, United States
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Phenotypic antibiotic susceptibility testing of pathogenic bacteria using photonic readout methods: recent achievements and impact. Appl Microbiol Biotechnol 2018; 103:549-566. [PMID: 30443798 DOI: 10.1007/s00253-018-9505-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 12/12/2022]
Abstract
The development of antibiotic resistances in common pathogens is an increasing challenge for therapy of infections and especially severe complications like sepsis. To prevent administration of broad-spectrum and potentially non-effective antibiotics, the susceptibility spectrum of the pathogens underlying the infection has to be determined. Current phenotypic standard methods for antibiotic susceptibility testing (AST) require the isolation of pathogens from the patient and the subsequent culturing in the presence of antibiotics leading to results only after 24-72 h. Since the early initialization of an effective antibiotic therapy is crucial for positive treatment result in severe infections, faster methods of AST are urgently needed. A large number of different assay systems are currently tested for their practicability for fast detection of antibiotic resistance profiles. They can be divided into genotypic ones which detect the presence of certain genes or gene products associated with resistances and phenotypic assays which determine the effect of antibiotics on the pathogens. In this mini-review, we summarize current developments in fast phenotypic tests that use photonic approaches and critically discuss their status. We further outline steps that are required to bring these assays into clinical practice.
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Chen L, Shin DJ, Zheng S, Melendez JH, Gaydos CA, Wang TH. Direct-qPCR Assay for Coupled Identification and Antimicrobial Susceptibility Testing of Neisseria gonorrhoeae. ACS Infect Dis 2018; 4:1377-1384. [PMID: 29999304 DOI: 10.1021/acsinfecdis.8b00104] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Multidrug-resistant gonorrhea has become an urgent issue for global public health. As the causative agent of gonorrhea, Neisseria gonorrhoeae, has been progressively developing resistance to nearly all prescribed antimicrobial drugs, monitoring its antimicrobial resistance on a broader scale has become a crucial agenda for effective antibiotic stewardship. Unfortunately, gold standard antimicrobial susceptibility testing (AST) relies on time and labor-intensive phenotypic assays, which lag behind the current diagnostic workflow for N. gonorrhoeae identification based on nucleic acid amplification tests (NAAT). Newer assay technologies based on NAAT can rapidly identify N. gonorrhoeae from clinical specimen but fundamentally lack the capacity to provide phenotypic AST information. Herein, we propose a direct-quantitative PCR (direct-qPCR) assay that enables pathogen-specific identification and phenotypic AST via quantitative measurement of N. gonorrhoeae growth directly from a liquid medium without any sample preprocessing. The assay has an analytical sensitivity of 102 CFU/mL and is highly specific to N. gonorrhoeae in the presence of urogenital flora and clinical swab eluent. We tested seven N. gonorrhoeae strains against three antibiotic agents, penicillin, tetracycline, and ciprofloxacin, and achieved 95.2% category agreement and 85.7% essential agreement with the FDA-approved E-test. The assay presented in this work has the unique ability to identify N. gonorrhoeae and provide phenotypic AST directly from the liquid medium with cell densities as low as 102 CFU/mL, demonstrating an accelerated, sensitive, and scalable workflow for performing both identification and AST of N. gonorrhoeae.
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Affiliation(s)
| | | | | | - Johan H. Melendez
- Division of Infectious Diseases, School of Medicine, Johns Hopkins University, 855 North Wolfe Street, Baltimore, Maryland 21205, United States
| | - Charlotte A. Gaydos
- Division of Infectious Diseases, School of Medicine, Johns Hopkins University, 855 North Wolfe Street, Baltimore, Maryland 21205, United States
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Sun Y, Heidary DK, Zhang Z, Richards CI, Glazer EC. Bacterial Cytological Profiling Reveals the Mechanism of Action of Anticancer Metal Complexes. Mol Pharm 2018; 15:3404-3416. [PMID: 29865789 PMCID: PMC6083414 DOI: 10.1021/acs.molpharmaceut.8b00407] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Target
identification and mechanistic studies of cytotoxic agents
are challenging processes that are both time-consuming and costly.
Here we describe an approach to mechanism of action studies for potential
anticancer compounds by utilizing the simple prokaryotic system, E. coli, and we demonstrate its utility with the characterization
of a ruthenium polypyridyl complex [Ru(bpy)2dmbpy2+]. Expression of the photoconvertible fluorescent protein Dendra2
facilitated both high throughput studies and single-cell imaging.
This allowed for simultaneous ratiometric analysis of inhibition of
protein production and phenotypic investigations. The profile of protein
production, filament size and population, and nucleoid morphology
revealed important differences between inorganic agents that damage
DNA vs more selective inhibitors of transcription and translation.
Trace metal analysis demonstrated that DNA is the preferred nucleic
acid target of the ruthenium complex, but further studies in human
cancer cells revealed altered cell signaling pathways compared to
the commonly administrated anticancer agent cisplatin. This study
demonstrates E. coli can be used to rapidly distinguish
between compounds with disparate mechanisms of action and also for
more subtle distinctions within in studies in mammalian cells.
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Affiliation(s)
- Yang Sun
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - David K Heidary
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Zhihui Zhang
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Christopher I Richards
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Edith C Glazer
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
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Antibiotic susceptibility testing in less than 30 min using direct single-cell imaging. Proc Natl Acad Sci U S A 2017; 114:9170-9175. [PMID: 28790187 DOI: 10.1073/pnas.1708558114] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The emergence and spread of antibiotic-resistant bacteria are aggravated by incorrect prescription and use of antibiotics. A core problem is that there is no sufficiently fast diagnostic test to guide correct antibiotic prescription at the point of care. Here, we investigate if it is possible to develop a point-of-care susceptibility test for urinary tract infection, a disease that 100 million women suffer from annually and that exhibits widespread antibiotic resistance. We capture bacterial cells directly from samples with low bacterial counts (104 cfu/mL) using a custom-designed microfluidic chip and monitor their individual growth rates using microscopy. By averaging the growth rate response to an antibiotic over many individual cells, we can push the detection time to the biological response time of the bacteria. We find that it is possible to detect changes in growth rate in response to each of nine antibiotics that are used to treat urinary tract infections in minutes. In a test of 49 clinical uropathogenic Escherichia coli (UPEC) isolates, all were correctly classified as susceptible or resistant to ciprofloxacin in less than 10 min. The total time for antibiotic susceptibility testing, from loading of sample to diagnostic readout, is less than 30 min, which allows the development of a point-of-care test that can guide correct treatment of urinary tract infection.
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Monitoring growth and antibiotic susceptibility of Escherichia coli with photoluminescence of GaAs/AlGaAs quantum well microstructures. Biosens Bioelectron 2017; 93:234-240. [DOI: 10.1016/j.bios.2016.08.112] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/17/2016] [Accepted: 08/31/2016] [Indexed: 12/31/2022]
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Leonard H, Halachmi S, Ben-Dov N, Nativ O, Segal E. Unraveling Antimicrobial Susceptibility of Bacterial Networks on Micropillar Architectures Using Intrinsic Phase-Shift Spectroscopy. ACS NANO 2017; 11:6167-6177. [PMID: 28485961 DOI: 10.1021/acsnano.7b02217] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
With global antimicrobial resistance becoming increasingly detrimental to society, improving current clinical antimicrobial susceptibility testing (AST) is crucial to allow physicians to initiate appropriate antibiotic treatment as early as possible, reducing not only mortality rates but also the emergence of resistant pathogens. In this work, we tackle the main bottlenecks in clinical AST by designing biofunctionalized silicon micropillar arrays to provide both a preferable solid-liquid interface for bacteria networking and a simultaneous transducing element that monitors the response of bacteria when exposed to chosen antibiotics in real time. We harness the intrinsic ability of the micropillar architectures to relay optical phase-shift reflectometric interference spectroscopic measurements (referred to as PRISM) and employ it as a platform for culture-free, label-free phenotypic AST. The responses of E. coli to various concentrations of five clinically relevant antibiotics are optically tracked by PRISM, allowing for the minimum inhibitory concentration (MIC) values to be determined and compared to both standard broth microdilution testing and clinic-based automated AST system readouts. Capture of bacteria within these microtopologies, followed by incubation of the cells with the appropriate antibiotic solution, yields rapid determinations of antibiotic susceptibility. This platform not only provides accurate MIC determinations in a rapid manner (total assay time of 2-3 h versus 8 h with automated AST systems) but can also be employed as an advantageous method to differentiate bacteriostatic and bactericidal antibiotics.
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Affiliation(s)
- Heidi Leonard
- Department of Biotechnology and Food Engineering, ‡Department of Urology, Bnai Zion Medical Center, Faculty of Medicine, and §The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology , Haifa 3200003, Israel
| | - Sarel Halachmi
- Department of Biotechnology and Food Engineering, ‡Department of Urology, Bnai Zion Medical Center, Faculty of Medicine, and §The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology , Haifa 3200003, Israel
| | - Nadav Ben-Dov
- Department of Biotechnology and Food Engineering, ‡Department of Urology, Bnai Zion Medical Center, Faculty of Medicine, and §The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology , Haifa 3200003, Israel
| | - Ofer Nativ
- Department of Biotechnology and Food Engineering, ‡Department of Urology, Bnai Zion Medical Center, Faculty of Medicine, and §The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology , Haifa 3200003, Israel
| | - Ester Segal
- Department of Biotechnology and Food Engineering, ‡Department of Urology, Bnai Zion Medical Center, Faculty of Medicine, and §The Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology , Haifa 3200003, Israel
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Grzybowski A, Brona P, Kim SJ. Microbial flora and resistance in ophthalmology: a review. Graefes Arch Clin Exp Ophthalmol 2017; 255:851-862. [PMID: 28229218 PMCID: PMC5394129 DOI: 10.1007/s00417-017-3608-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/11/2017] [Accepted: 02/06/2017] [Indexed: 02/03/2023] Open
Abstract
Antibiotic resistance in systemic infection is well-researched and well-publicized. Much less information is available on the resistance of normal ocular microbiome and that of ophthalmic infections. An understanding of the distribution of ocular microorganisms may help us in tailoring our empiric treatment, as well as in choosing effective pre-, peri- and postoperative management, to achieve the best results for patients. This study aims to summarize and review the available literature on the subject of normal ocular flora and its resistance, as well as the broader topic of antibiotic resistance in ophthalmology.
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Affiliation(s)
- Andrzej Grzybowski
- Department of Ophthalmology, Poznan City Hospital, Ul. Szwajcarska 3, 60-285, Poznan, Poland.
- Department of Ophthalmology, University of Warmia and Mazury, Olsztyn, Poland.
| | - Piotr Brona
- Department of Ophthalmology, Poznan City Hospital, Ul. Szwajcarska 3, 60-285, Poznan, Poland
| | - Stephen Jae Kim
- Department of Ophthalmology, Vanderbilt University, Nashville, TN, USA
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Syal K, Mo M, Yu H, Iriya R, Jing W, Guodong S, Wang S, Grys TE, Haydel SE, Tao N. Current and emerging techniques for antibiotic susceptibility tests. Theranostics 2017; 7:1795-1805. [PMID: 28638468 PMCID: PMC5479269 DOI: 10.7150/thno.19217] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/03/2017] [Indexed: 12/23/2022] Open
Abstract
Infectious diseases caused by bacterial pathogens are a worldwide burden. Serious bacterial infection-related complications, such as sepsis, affect over a million people every year with mortality rates ranging from 30% to 50%. Crucial clinical microbiology laboratory responsibilities associated with patient management and treatment include isolating and identifying the causative bacterium and performing antibiotic susceptibility tests (ASTs), which are labor-intensive, complex, imprecise, and slow (taking days, depending on the growth rate of the pathogen). Considering the life-threatening condition of a septic patient and the increasing prevalence of antibiotic-resistant bacteria in hospitals, rapid and automated diagnostic tools are needed. This review summarizes the existing commercial AST methods and discusses some of the promising emerging AST tools that will empower humans to win the evolutionary war between microbial genes and human wits.
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Affiliation(s)
- Karan Syal
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Manni Mo
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
| | - Hui Yu
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Rafael Iriya
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
| | - Wenwen Jing
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Sui Guodong
- Institute of Biomedical Science, Fudan University, Shanghai, China
| | - Shaopeng Wang
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Thomas E. Grys
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Phoenix, Arizona 85054, USA
| | - Shelley E. Haydel
- Center for Immunotherapy, Vaccines, and Virotherapy, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Nongjian Tao
- Center for Biosensors and Bioelectronics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
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Wang C, Yang X, Mellick GD, Feng Y. Meeting the Challenge: Using Cytological Profiling to Discover Chemical Probes from Traditional Chinese Medicines against Parkinson's Disease. ACS Chem Neurosci 2016; 7:1628-1634. [PMID: 27736095 DOI: 10.1021/acschemneuro.6b00245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Parkinson's disease (PD) is an incurable neurodegenerative disorder with a high prevalence rate worldwide. The fact that there are currently no proven disease-modifying treatments for PD underscores the urgency for a more comprehensive understanding of the underlying disease mechanism. Chemical probes have been proven to be powerful tools for studying biological processes. Traditional Chinese medicine (TCM) contains a huge reservoir of bioactive small molecules as potential chemical probes that may hold the key to unlocking the mystery of PD biology. The TCM-sourced chemical approach to PD biology can be advanced through the use of an emerging cytological profiling (CP) technique that allows unbiased characterization of small molecules and their cellular responses. This comprehensive technique, applied to chemical probe identification from TCM and used for studying the molecular mechanisms underlying PD, may inform future therapeutic target selection and provide a new perspective to PD drug discovery.
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Affiliation(s)
- Chao Wang
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Xinzhou Yang
- College of Pharmacy, South-Central University for Nationalities, Wuhan 430074, China
| | - George D. Mellick
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Yunjiang Feng
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
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Cefazolin and Ertapenem, a Synergistic Combination Used To Clear Persistent Staphylococcus aureus Bacteremia. Antimicrob Agents Chemother 2016; 60:6609-6618. [PMID: 27572414 PMCID: PMC5075066 DOI: 10.1128/aac.01192-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 08/08/2016] [Indexed: 11/22/2022] Open
Abstract
Ertapenem and cefazolin were used in combination to successfully clear refractory methicillin-susceptible Staphylococcus aureus (MSSA) bacteremia. In addition, recent work has demonstrated activity of combination therapy with beta-lactams from different classes against methicillin-resistant S. aureus (MRSA). The ertapenem-plus-cefazolin combination was evaluated for synergy in vitro and in vivo in a murine skin infection model using an index MSSA bloodstream isolate from a patient in whom persistent bacteremia was cleared with this combination and against a cadre of well-described research strains and clinical strains of MSSA and MRSA. Against the index MSSA bloodstream isolate, ertapenem and cefazolin showed synergy using both checkerboard (fractional inhibitory concentration [FIC] index = 0.375) and time-kill assays. Using a disk diffusion ertapenem potentiation assay, the MSSA isolate showed a cefazolin disk zone increased from 34 to 40 mm. In vitro pharmacokinetic/pharmacodynamic modeling at clinically relevant drug concentrations demonstrated bactericidal activity (>3 log10-CFU/ml reduction) of the combination but bacteriostatic activity of ether drug alone at 48 h. A disk diffusion potentiation assay showed that ertapenem increased the cefazolin zone of inhibition by >3 mm for 34/35 (97%) MSSA and 10/15 (67%) MRSA strains. A murine skin infection model of MSSA showed enhanced activity of cefazolin plus ertapenem compared to monotherapy with these agents. After successful use in clearance of MSSA bacteremia, the combination of ertapenem and cefazolin showed synergy against MSSA in vitro and in vivo. This combination may warrant consideration for future clinical study in MSSA bacteremia.
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50
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Araújo-Bazán L, Ruiz-Avila LB, Andreu D, Huecas S, Andreu JM. Cytological Profile of Antibacterial FtsZ Inhibitors and Synthetic Peptide MciZ. Front Microbiol 2016; 7:1558. [PMID: 27752253 PMCID: PMC5045927 DOI: 10.3389/fmicb.2016.01558] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/16/2016] [Indexed: 11/26/2022] Open
Abstract
Cell division protein FtsZ is the organizer of the cytokinetic ring in almost all bacteria and a target for the discovery of new antibacterial agents that are needed to counter widespread antibiotic resistance. Bacterial cytological profiling, using quantitative microscopy, is a powerful approach for identifying the mechanism of action of antibacterial molecules affecting different cellular pathways. We have determined the cytological profile on Bacillus subtilis cells of a selection of small molecule inhibitors targeting FtsZ on different binding sites. FtsZ inhibitors lead to long undivided cells, impair the normal assembly of FtsZ into the midcell Z-rings, induce aberrant ring distributions, punctate FtsZ foci, membrane spots and also modify nucleoid length. Quantitative analysis of cell and nucleoid length combined, or the Z-ring distribution, allows categorizing FtsZ inhibitors and to distinguish them from antibiotics with other mechanisms of action, which should be useful for identifying new antibacterial FtsZ inhibitors. Biochemical assays of FtsZ polymerization and GTPase activity combined explain the cellular effects of the FtsZ polymer stabilizing agent PC190723 and its fragments. MciZ is a 40-aminoacid endogenous inhibitor of cell division normally expressed during sporulation in B. subtilis. Using FtsZ cytological profiling we have determined that exogenous synthetic MciZ is an effective inhibitor of B. subtilis cell division, Z-ring formation and localization. This finding supports our cell-based approach to screen for FtsZ inhibitors and opens new possibilities for peptide inhibitors of bacterial cell division.
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Affiliation(s)
- Lidia Araújo-Bazán
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Laura B Ruiz-Avila
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - David Andreu
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra Barcelona, Spain
| | - Sonia Huecas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - José M Andreu
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
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