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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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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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3
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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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4
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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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5
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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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6
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Cabezas-Mera FS, Atiencia-Carrera MB, Villacrés-Granda I, Proaño AA, Debut A, Vizuete K, Herrero-Bayo L, Gonzalez-Paramás AM, Giampieri F, Abreu-Naranjo R, Tejera E, Álvarez-Suarez JM, Machado A. Evaluation of the polyphenolic profile of native Ecuadorian stingless bee honeys ( Tribe: Meliponini) and their antibiofilm activity on susceptible and multidrug-resistant pathogens: An exploratory analysis. Curr Res Food Sci 2023; 7:100543. [PMID: 37455680 PMCID: PMC10344713 DOI: 10.1016/j.crfs.2023.100543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/08/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
Biofilms are associated with infections that are resistant to conventional therapies, contributing to the antimicrobial resistance crisis. The need for alternative approaches against biofilms is well-known. Although natural products like stingless bee honeys (tribe: Meliponini) constitute an alternative treatment, much is still unknown. Our main goal was to evaluate the antibiofilm activity of stingless bee honey samples against multidrug-resistant (MDR) pathogens through biomass assays, fluorescence (cell count and viability), and scanning electron (structural composition) microscopy. We analyzed thirty-five honey samples at 15% (v/v) produced by ten different stingless bee species (Cephalotrigona sp., Melipona sp., M. cramptoni, M. fuscopilosa, M. grandis, M. indecisa, M. mimetica, M. nigrifacies, Scaptotrigona problanca, and Tetragonisca angustula) from five provinces of Ecuador (Tungurahua, Pastaza, El Oro, Los Ríos, and Loja) against 24-h biofilms of Staphylococcus aureus, Klebsiella pneumoniae, Candida albicans, and Candida tropicalis. The present honey set belonged to our previous study, where the samples were collected in 2018-2019 and their physicochemical parameters, chemical composition, mineral elements, and minimal inhibitory concentration (MIC) were screened. However, the polyphenolic profile and their antibiofilm activity on susceptible and multidrug-resistant pathogens were still unknown. According to polyphenolic profile of the honey samples, significant differences were observed according to their geographical origin in terms of the qualitative profiles. The five best honey samples (OR24.1, LR34, LO40, LO48, and LO53) belonging to S. problanca, Melipona sp., and M. indecisa were selected for further analysis due to their high biomass reduction values, identification of the stingless bee specimens, and previously reported physicochemical parameters. This subset of honey samples showed a range of 63-80% biofilm inhibition through biomass assays. Fluorescence microscopy (FM) analysis evidenced statistical log reduction in the cell count of honey-treated samples in all pathogens (P <0.05), except for S. aureus ATCC 25923. Concerning cell viability, C. tropicalis, K. pneumoniae ATCC 33495, and K. pneumoniae KPC significantly decreased (P <0.01) by 21.67, 25.69, and 45.62%, respectively. Finally, scanning electron microscopy (SEM) analysis demonstrated structural biofilm disruption through cell morphological parameters (such as area, size, and form). In relation to their polyphenolic profile, medioresinol was only found in the honey of Loja, while scopoletin, kaempferol, and quercetin were only identified in honey of Los Rios, and dihydrocaffeic and dihydroxyphenylacetic acids were only detected in honey of El Oro. All the five honey samples showed dihydrocoumaroylhexose, luteolin, and kaempferol rutinoside. To the authors' best knowledge, this is the first study to analyze stingless bees honey-treated biofilms of susceptible and/or MDR strains of S. aureus, K. pneumoniae, and Candida species.
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Affiliation(s)
- Fausto Sebastián Cabezas-Mera
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto de Microbiología, Laboratorio de Bacteriología, Calle Diego de Robles y Pampite, Quito, 170901, Ecuador
| | - María Belén Atiencia-Carrera
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto de Microbiología, Laboratorio de Bacteriología, Calle Diego de Robles y Pampite, Quito, 170901, Ecuador
| | - Irina Villacrés-Granda
- Programa de Doctorado Interuniversitario en Ciencias de la Salud, Universidad de Sevilla, Sevilla, Spain
- Facultad de Ingeniería y Ciencias Agropecuarias Aplicadas, Grupo de Bioquimioinformática, Universidad de Las Américas (UDLA), De Los Colimes esq, Quito, 170513, Quito, Ecuador
| | - Adrian Alexander Proaño
- Laboratorios de Investigación, Universidad de Las Américas (UDLA), Vía a Nayón, Quito, 170124, Ecuador
| | - Alexis Debut
- Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolquí, 171103, Ecuador
- Centro de Nanociencia y Nanotecnología, Universidad de Las Fuerzas Armadas ESPE, Sangolquí, 171103, Ecuador
| | - Karla Vizuete
- Centro de Nanociencia y Nanotecnología, Universidad de Las Fuerzas Armadas ESPE, Sangolquí, 171103, Ecuador
| | - Lorena Herrero-Bayo
- Grupo de Investigación en Polifenoles (GIP-USAL), Universidad de Salamanca, Campus Miguel de Unamuno, 37008, Salamanca, Spain
| | - Ana M. Gonzalez-Paramás
- Grupo de Investigación en Polifenoles (GIP-USAL), Universidad de Salamanca, Campus Miguel de Unamuno, 37008, Salamanca, Spain
| | - Francesca Giampieri
- Research Group on Food, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, C. Isabel Torres, 21, 39011, Santander, Cantabria, Spain
| | - Reinier Abreu-Naranjo
- Departamento de Ciencias de La Vida, Universidad Estatal Amazónica, Puyo, 160150, Ecuador
| | - Eduardo Tejera
- Facultad de Ingeniería y Ciencias Agropecuarias Aplicadas, Grupo de Bioquimioinformática, Universidad de Las Américas (UDLA), De Los Colimes esq, Quito, 170513, Quito, Ecuador
| | - José M. Álvarez-Suarez
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias e Ingenierías, Departamento de Ingeniería en Alimentos, Calle Diego de Robles y Pampite, Quito, 170901, Ecuador
| | - António Machado
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto de Microbiología, Laboratorio de Bacteriología, Calle Diego de Robles y Pampite, Quito, 170901, Ecuador
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7
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Asp ME, Thanh MTH, Dutta S, Comstock JA, Welch RD, Patteson AE. Mechanobiology as a tool for addressing the genotype-to-phenotype problem in microbiology. BIOPHYSICS REVIEWS 2023; 4:021304. [PMID: 38504926 PMCID: PMC10903382 DOI: 10.1063/5.0142121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/03/2023] [Indexed: 03/21/2024]
Abstract
The central hypothesis of the genotype-phenotype relationship is that the phenotype of a developing organism (i.e., its set of observable attributes) depends on its genome and the environment. However, as we learn more about the genetics and biochemistry of living systems, our understanding does not fully extend to the complex multiscale nature of how cells move, interact, and organize; this gap in understanding is referred to as the genotype-to-phenotype problem. The physics of soft matter sets the background on which living organisms evolved, and the cell environment is a strong determinant of cell phenotype. This inevitably leads to challenges as the full function of many genes, and the diversity of cellular behaviors cannot be assessed without wide screens of environmental conditions. Cellular mechanobiology is an emerging field that provides methodologies to understand how cells integrate chemical and physical environmental stress and signals, and how they are transduced to control cell function. Biofilm forming bacteria represent an attractive model because they are fast growing, genetically malleable and can display sophisticated self-organizing developmental behaviors similar to those found in higher organisms. Here, we propose mechanobiology as a new area of study in prokaryotic systems and describe its potential for unveiling new links between an organism's genome and phenome.
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Zhou Y, Xiong D, Guo Y, Liu Y, Kang X, Song H, Jiao X, Pan Z. Salmonella Enteritidis RfbD enhances bacterial colonization and virulence through inhibiting autophagy. Microbiol Res 2023; 270:127338. [PMID: 36854232 DOI: 10.1016/j.micres.2023.127338] [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: 01/03/2023] [Revised: 01/22/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
Autophagy is a crucial innate immune response that clears pathogens intracellularly. Salmonella enterica serovar Enteritidis (S.E) has emerged as one of the most important food-borne pathogens. Here, we reported that dTDP-4-dehydro-β-ւ-rhamnose reductase (RfbD) was able to enhance bacterial colonization in vivo and in vitro by regulating autophagy. We screened the transposon mutant library of Salmonella Enteritidis strain Z11 by High-Content Analysis System, found that rfbD gene has an effect on autophagy. The Z11ΔrfbD-infected group showed greater expression of LC3-II than the Z11-infected group in HeLa, RAW264.7, and J774A.1 cells. Overall, the survival of Z11ΔrfbD in RAW264.7 cells was reduced after 8 h of infection compared to that of the Z11 wild-type strain. In addition, we observed that inhibition of autophagic flux significantly increased the survival of Z11ΔrfbD in RAW264.7 cells. Mice infection experiments revealed that Z11ΔrfbD virulence was significantly reduced, and bacterial load was reduced in the liver and cecum in mice model, and LC3-II expression was significantly increased. These findings indicate an important role of Salmonella Enteritidis protein as a strategy to suppress autophagy and provides new ideas for manipulating autophagy as a novel strategy to treat infectious diseases.
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Affiliation(s)
- Yi Zhou
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Dan Xiong
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yaxin Guo
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yi Liu
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xilong Kang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China
| | - Hongqin Song
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Zhiming Pan
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, Jiangsu, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, Jiangsu, China; Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of A griculture of China, Yangzhou University, Yangzhou, Jiangsu, China; Joint International Research Laboratory of Agriculture and Agri-product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu, China.
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9
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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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High-Resolution Bacterial Cytological Profiling Reveals Intrapopulation Morphological Variations upon Antibiotic Exposure. Antimicrob Agents Chemother 2023; 67:e0130722. [PMID: 36625642 PMCID: PMC9933734 DOI: 10.1128/aac.01307-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Phenotypic heterogeneity is crucial to bacterial survival and could provide insights into the mechanism of action (MOA) of antibiotics, especially those with polypharmacological actions. Although phenotypic changes among individual cells could be detected by existing profiling methods, due to the data complexity, only population average data were commonly used, thereby overlooking the heterogeneity. In this study, we developed a high-resolution bacterial cytological profiling method that can capture morphological variations of bacteria upon antibiotic treatment. With an unprecedented single-cell resolution, this method classifies morphological changes of individual cells into known MOAs with an overall accuracy above 90%. We next showed that combinations of two antibiotics induce altered cell morphologies that are either unique or similar to that of an antibiotic in the combinations. With these combinatorial profiles, this method successfully revealed multiple cytological changes caused by a natural product-derived compound that, by itself, is inactive against Acinetobacter baumannii but synergistically exerts its multiple antibacterial activities in the presence of colistin. The findings have paved the way for future single-cell profiling in bacteria and have highlighted previously underappreciated intrapopulation variations caused by antibiotic perturbation.
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11
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Unleashing high content screening in hit detection – benchmarking AI workflows including novelty detection. Comput Struct Biotechnol J 2022; 20:5453-5465. [PMID: 36212538 PMCID: PMC9530837 DOI: 10.1016/j.csbj.2022.09.023] [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: 06/30/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022] Open
Abstract
Complex mixtures containing natural products are still an interesting source of novel drug candidates. High content screening (HCS) is a popular tool to screen for such. In particular, multiplexed HCS assays promise comprehensive bioactivity profiles, but generate also high amounts of data. Yet, only some machine learning (ML) applications for data analysis are available and these usually require a profound knowledge of the underlying cell biology. Unfortunately, there are no applications that simply predict if samples are biologically active or not (any kind of bioactivity). Within this work, we benchmark ML algorithms for binary classification, starting with classical ML models, which are the standard classifiers of the scikit-learn library or ensemble models of these classifiers (a total of 92 models tested). Followed by a partial least square regression (PLSR)-based classification (44 tested models in total) and simple artificial neural networks (ANNs) with dense layers (72 tested models in total). In addition, a novelty detection (ND) was examined, which is supposed to handle unknown patterns. For the final analysis the models, with and without upstream ND, were tested with two independent data sets. In our analysis, a stacking model, an ensamble model of class ML algorithms, performed best to predict new and unknown data. ND improved the predictions of the models and was useful to handle unknown patterns. Importantly, the classifier presented here can be easily rebuilt and be adapted to the data and demands of other groups. The hit detector (ND + stacking model) is universal and suitable for a broader application to support the search for new drug candidates.
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12
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Phillips SMB, Bergstrom C, Walker B, Wang G, Alfaro T, Stromberg ZR, Hess BM. Engineered Cell Line Imaging Assay Differentiates Pathogenic from Non-Pathogenic Bacteria. Pathogens 2022; 11:pathogens11020209. [PMID: 35215152 PMCID: PMC8874627 DOI: 10.3390/pathogens11020209] [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: 12/08/2021] [Revised: 01/31/2022] [Accepted: 02/02/2022] [Indexed: 01/27/2023] Open
Abstract
Cell culture systems have greatly expanded our understanding of how bacterial pathogens target signaling pathways to manipulate the host and cause infection. Advances in genetic engineering have allowed for the creation of fluorescent protein readouts within signaling pathways, but these techniques have been underutilized in pathogen biology. Here, we genetically engineered a lung cell line with fluorescent reporters for extracellular signal-related kinase (ERK) and the downstream transcription factor FOS-related antigen 1 (Fra1) and evaluated signaling after inoculation with pathogenic and non-pathogenic bacteria. Cells were inoculated with 100 colony-forming units of Acinetobacter baylyi, Klebsiella pneumoniae, Pseudomonas aeruginosa, Streptococcus agalactiae, or Staphylococcus epidermidis and imaged in a multi-mode reader. The alamarBlue cell viability assay was used as a reference test and showed that pathogenic P. aeruginosa induced significant (p < 0.05) cell death after 8 h in both wild-type and engineered cell lines compared to non-pathogenic S. epidermidis. In engineered cells, we found that Fra1 signaling was disrupted in as little as 4 h after inoculation with bacterial pathogens compared to delayed disruption in signaling by non-pathogenic S. epidermidis. Overall, we demonstrate that low levels of pathogenic versus non-pathogenic bacteria can be rapidly and sensitively screened based on ERK-Fra1 signaling.
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13
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Coram MA, Wang L, Godinez WJ, Barkan DT, Armstrong Z, Ando DM, Feng BY. Morphological Characterization of Antibiotic Combinations. ACS Infect Dis 2022; 8:66-77. [PMID: 34937332 DOI: 10.1021/acsinfecdis.1c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Combination therapies are common in many therapeutic contexts, including infectious diseases and cancer. A common approach for evaluating combinations in vitro is to assess effects on cell growth as synergistic, antagonistic, or neutral using "checkerboard" experiments to systematically sample combinations of agents in multiple doses. To further understand the effects of antibiotic combinations, we employed high-content imaging to study the morphological changes caused by combination treatments in checkerboard experiments. Using an automated, unsupervised image analysis approach to group morphologies, and an "expert-in-the-loop" to annotate them, we attributed the heterogeneous morphological changes ofEscherichia coli cells to varying doses of both single-agent and combination treatments. We identified patterns of morphological change, including morphological potentiation, competition, and the emergence of unexpected morphologies. We found these frequently did not correlate with synergistic or antagonistic effects on viability, suggesting morphological approaches may provide a distinctive signature of the biological interaction between compounds over a range of conditions. Among the unexpected morphologies we observed, there were transitional changes associated with intermediate doses of compounds and uncharacterized phenotypes associated with well-studied antibiotics. Our approach exemplifies how unsupervised image analysis and expert knowledge can be combined to reckon with complex phenotypic changes arising from combination screening, dose titrations, or polypharmacology. In this way, quantification of morphological diversity across treatment conditions could aid in analysis and prioritization of complementary pairings of antibiotic agents by more closely capturing the true signature of the integrated cellular response.
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Affiliation(s)
- Marc A. Coram
- Google Research Applied Science, Mountain View, California 94043, United States
| | - Lisha Wang
- Infectious Diseases, Novartis Institutes for BioMedical Research, Inc., Emeryville, California 94608, United States
| | - William J. Godinez
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Inc., Emeryville, California 94608, United States
| | - David T. Barkan
- Chemical Biology & Therapeutics, Novartis Institutes for BioMedical Research, Inc., Emeryville, California 94608, United States
| | - Zan Armstrong
- Google Research Applied Science, Mountain View, California 94043, United States
| | - D. Michael Ando
- Google Research Applied Science, Mountain View, California 94043, United States
| | - Brian Y. Feng
- Infectious Diseases, Novartis Institutes for BioMedical Research, Inc., Emeryville, California 94608, United States
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14
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Sridhar S, Forrest S, Pickard D, Cormie C, Lees EA, Thomson NR, Dougan G, Baker S. Inhibitory Concentrations of Ciprofloxacin Induce an Adaptive Response Promoting the Intracellular Survival of Salmonella enterica Serovar Typhimurium. mBio 2021; 12:e0109321. [PMID: 34154399 PMCID: PMC8262899 DOI: 10.1128/mbio.01093-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/19/2021] [Indexed: 12/02/2022] Open
Abstract
Antimicrobial resistance (AMR) is a pressing global health crisis, which has been fueled by the sustained use of certain classes of antimicrobials, including fluoroquinolones. While the genetic mutations responsible for decreased fluoroquinolone (ciprofloxacin) susceptibility are known, the implications of ciprofloxacin exposure on bacterial growth, survival, and interactions with host cells are not well described. Aiming to understand the influence of inhibitory concentrations of ciprofloxacin in vitro, we subjected three clinical isolates of Salmonella enterica serovar Typhimurium to differing concentrations of ciprofloxacin, dependent on their MICs, and assessed the impact on bacterial growth, morphology, and transcription. We further investigated the differential morphology and transcription that occurred following ciprofloxacin exposure and measured the ability of ciprofloxacin-treated bacteria to invade and replicate in host cells. We found that ciprofloxacin-exposed S. Typhimurium is able to recover from inhibitory concentrations of ciprofloxacin and that the drug induces specific morphological and transcriptional signatures associated with the bacterial SOS response, DNA repair, and intracellular survival. In addition, ciprofloxacin-treated S. Typhimurium has increased capacity for intracellular replication in comparison to that of untreated organisms. These data suggest that S. Typhimurium undergoes an adaptive response under ciprofloxacin perturbation that promotes cellular survival, a consequence that may justify more measured use of ciprofloxacin for Salmonella infections. The combination of multiple experimental approaches provides new insights into the collateral effects that ciprofloxacin and other antimicrobials have on invasive bacterial pathogens. IMPORTANCE Antimicrobial resistance is a critical concern in global health. In particular, there is rising resistance to fluoroquinolones, such as ciprofloxacin, a first-line antimicrobial for many Gram-negative pathogens. We investigated the adaptive response of clinical isolates of Salmonella enterica serovar Typhimurium to ciprofloxacin, finding that the bacteria adapt in short timespans to high concentrations of ciprofloxacin in a way that promotes intracellular survival during early infection. Importantly, by studying three clinically relevant isolates, we were able to show that individual isolates respond differently to ciprofloxacin and that for each isolate, there was a heterogeneous response under ciprofloxacin treatment. The heterogeneity that arises from ciprofloxacin exposure may drive survival and proliferation of Salmonella during treatment and lead to drug resistance.
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Affiliation(s)
- Sushmita Sridhar
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Sally Forrest
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Derek Pickard
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Claire Cormie
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Emily A. Lees
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - Nicholas R. Thomson
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gordon Dougan
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Stephen Baker
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
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15
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Haddad G, Fontanini A, Bellali S, Takakura T, Ominami Y, Hisada A, Hadjadj L, Rolain JM, Raoult D, Bou Khalil JY. Rapid Detection of Imipenem Resistance in Gram-Negative Bacteria Using Tabletop Scanning Electron Microscopy: A Preliminary Evaluation. Front Microbiol 2021; 12:658322. [PMID: 34220746 PMCID: PMC8245003 DOI: 10.3389/fmicb.2021.658322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/18/2021] [Indexed: 12/29/2022] Open
Abstract
Background: Enabling faster Antimicrobial Susceptibility Testing (AST) is critical, especially to detect antibiotic resistance, to provide rapid and appropriate therapy and to improve clinical outcomes. Although several standard and automated culture-based methods are available and widely used, these techniques take between 18 and 24 h to provide robust results. Faster techniques are needed to reduce the delay between test and results. Methods: Here we present a high throughput AST method using a new generation of tabletop scanning electron microscope, to evaluate bacterial ultra-structural modifications associated with susceptibilities to imipenem as a proof of concept. A total of 71 reference and clinical strains of Gram-negative bacteria were used to evaluate susceptibility toward imipenem after 30, 60, and 90 min of incubation. The length, width and electron density of bacteria were measured and compared between imipenem susceptible and resistant strains. Results: We correlated the presence of these morphological changes to the bacterial susceptibility and their absence to the bacterial resistance (e.g., Pseudomonas aeruginosa length without [2.24 ± 0.61 μm] and with [2.50 ± 0.68 μm] imipenem after 30 min [p = 3.032E-15]; Escherichia coli width without [0.92 ± 0.07 μm] and with [1.28 ± 0.19 μm] imipenem after 60 min [p = 1.242E-103]). We validated our method by a blind test on a series of 58 clinical isolates where all strains were correctly classified as susceptible or resistant toward imipenem. Conclusion: This method could be a potential tool for rapidly identifying carbapenem-resistance in Enterobacterales in clinical microbiology laboratories in <2 h, allowing the empirical treatment of patients to be rapidly adjusted.
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Affiliation(s)
- Gabriel Haddad
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Anthony Fontanini
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Sara Bellali
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Tatsuki Takakura
- Hitachi High-Tech Corporation, Analytical & Medical Solution Business Group, Ibaraki, Japan
| | - Yusuke Ominami
- Hitachi High-Tech Corporation, Nanotechnology Solutions Business Group, Toranomon Hills Business Tower, Tokyo, Japan
| | - Akiko Hisada
- Hitachi, Ltd., Research & Development Group, Tokyo, Japan
| | - Linda Hadjadj
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France.,Hitachi High-Tech Corporation, Nanotechnology Solutions Business Group, Toranomon Hills Business Tower, Tokyo, Japan
| | - Jacques Yaacoub Bou Khalil
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France.,Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), UMR Microbes Evolution Phylogeny and Infections (MEPHI), Marseille, France
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