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Li X, Liu X, Yu Z, Luo Y, Hu Q, Xu Z, Dai J, Wu N, Shen F. Combinatorial screening SlipChip for rapid phenotypic antimicrobial susceptibility testing. LAB ON A CHIP 2022; 22:3952-3960. [PMID: 36106408 DOI: 10.1039/d2lc00661h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Antimicrobial resistance (AMR) by bacteria is a serious global threat, and a rapid, high-throughput, and easy-to-use phenotypic antimicrobial susceptibility testing (AST) method is essential for making timely treatment decisions and controlling the spread of antibiotic resistant micro-organisms. Traditional culture-based methods are time-consuming, and their capability to screen against a large number of different conditions is limited; meanwhile genotypic based methods, including sequencing and PCR based methods, are constrained by rarely identified resistance genes and complicated resistance mechanisms. Here, a combinatorial-screening SlipChip (cs-SlipChip) containing 192 nanoliter-sized compartments is developed which can perform high-throughput phenotypic AST within three hours by monitoring the bacterial growth within nanoliter-sized droplets with bright-field imaging and analyzing the changes in bacterial number and morphology. The minimum inhibitory concentration (MIC) of Escherichia coli ATCC 25922 against four antibiotics (ampicillin, ciprofloxacin, ceftazidime, and nitrofurantoin) can be measured in one chip within 3 hours. Furthermore, five antibiotic-resistant E. coli strains were isolated from patients diagnosed with urinary tract infections (UTIs), and an individual isolate was tested using four antibiotics and eleven antibiotic combinations simultaneously with three different concentrations of each. The results from the cs-SlipChip agree with those of a VITEK 2 automated system. This cs-SlipChip provides a practical high-throughput and rapid phenotypic method for AST and can also be used to screen different chemicals and antibiotic combinations for the treatment of multiple antibiotic-resistant bacteria.
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Affiliation(s)
- Xiang Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Xu Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Ziqing Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Yang Luo
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Qixin Hu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Zhenye Xu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
| | - Jia Dai
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Nannan Wu
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
- CreatiPhage Biotechnology Co., Ltd, Shanghai, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, China.
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52
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Postek W, Pacocha N, Garstecki P. Microfluidics for antibiotic susceptibility testing. LAB ON A CHIP 2022; 22:3637-3662. [PMID: 36069631 DOI: 10.1039/d2lc00394e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The rise of antibiotic resistance is a threat to global health. Rapid and comprehensive analysis of infectious strains is critical to reducing the global use of antibiotics, as informed antibiotic use could slow down the emergence of resistant strains worldwide. Multiple platforms for antibiotic susceptibility testing (AST) have been developed with the use of microfluidic solutions. Here we describe microfluidic systems that have been proposed to aid AST. We identify the key contributions in overcoming outstanding challenges associated with the required degree of multiplexing, reduction of detection time, scalability, ease of use, and capacity for commercialization. We introduce the reader to microfluidics in general, and we analyze the challenges and opportunities related to the field of microfluidic AST.
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Affiliation(s)
- Witold Postek
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
- Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA 02142, USA.
| | - Natalia Pacocha
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
| | - Piotr Garstecki
- Institute of Physical Chemistry of the Polish Academy of Sciences, ul. Kasprzaka 44/52, 01-224 Warszawa, Poland.
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Bassetti M, Kanj SS, Kiratisin P, Rodrigues C, Van Duin D, Villegas MV, Yu Y. Early appropriate diagnostics and treatment of MDR Gram-negative infections. JAC Antimicrob Resist 2022; 4:dlac089. [PMID: 36111208 PMCID: PMC9469888 DOI: 10.1093/jacamr/dlac089] [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] [Indexed: 11/16/2022] Open
Abstract
The term difficult-to-treat resistance has been recently coined to identify Gram-negative bacteria exhibiting resistance to all fluoroquinolones and all β-lactam categories, including carbapenems. Such bacteria are posing serious challenges to clinicians trying to identify the best therapeutic option for any given patient. Delayed appropriate therapy has been associated with worse outcomes including increase in length of stay, increase in total in-hospital costs and ∼20% increase in the risk of in-hospital mortality. In addition, time to appropriate antibiotic therapy has been shown to be an independent predictor of 30 day mortality in patients with resistant organisms. Improving and anticipating aetiological diagnosis through optimizing not only the identification of phenotypic resistance to antibiotic classes/agents, but also the identification of specific resistance mechanisms, would have a major impact on reducing the frequency and duration of inappropriate early antibiotic therapy. In light of these considerations, the present paper reviews the increasing need for rapid diagnosis of bacterial infections and efficient laboratory workflows to confirm diagnoses and facilitate prompt de-escalation to targeted therapy, in line with antimicrobial stewardship principles. Rapid diagnostic tests currently available and future perspectives for their use are discussed. Early appropriate diagnostics and treatment of MDR Gram-negative infections require a multidisciplinary approach that includes multiple different diagnostic methods and further consensus of algorithms, protocols and guidelines to select the optimal antibiotic therapy.
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Affiliation(s)
- Matteo Bassetti
- Department of Health Science, University of Genoa , Italy
- Infectious Diseases Clinic, Ospedale Policlinico San Martino Hospital – IRCCS , Genoa , Italy
| | - Souha S Kanj
- Division of Infectious Diseases, American University of Beirut Medical Center , Beirut , Lebanon
| | - Pattarachai Kiratisin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok , Thailand
| | - Camilla Rodrigues
- Department of Microbiology, P. D. Hinduja Hospital and Medical Research Centre , Mumbai, Maharashtra , India
| | - David Van Duin
- Department of Medicine, University of North Carolina School of Medicine , Chapel Hill, NC , USA
| | - María Virginia Villegas
- Grupo de Investigaciones en Resistencia Antimicrobiana y Epidemiología Hospitalaria (RAEH), Universidad El Bosque , Bogotá DC , Colombia
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou, Zhejiang , China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province , Hangzhou, Zhejiang , China
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54
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Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics. Int J Mol Sci 2022; 23:ijms23179834. [PMID: 36077231 PMCID: PMC9456280 DOI: 10.3390/ijms23179834] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 12/21/2022] Open
Abstract
Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.
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Zhang W, Sun H, He S, Chen X, Yao L, Zhou L, Wang Y, Wang P, Hong W. Compound Raman microscopy for rapid diagnosis and antimicrobial susceptibility testing of pathogenic bacteria in urine. Front Microbiol 2022; 13:874966. [PMID: 36090077 PMCID: PMC9449455 DOI: 10.3389/fmicb.2022.874966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022] Open
Abstract
Rapid identification and antimicrobial susceptibility testing (AST) of bacteria are key interventions to curb the spread and emergence of antimicrobial resistance. The current gold standard identification and AST methods provide comprehensive diagnostic information but often take 3 to 5 days. Here, a compound Raman microscopy (CRM), which integrates Raman spectroscopy and stimulated Raman scattering microscopy in one system, is presented and demonstrated for rapid identification and AST of pathogens in urine. We generated an extensive bacterial Raman spectral dataset and applied deep learning to identify common clinical bacterial pathogens. In addition, we employed stimulated Raman scattering microscopy to quantify bacterial metabolic activity to determine their antimicrobial susceptibility. For proof-of-concept, we demonstrated an integrated assay to diagnose urinary tract infection pathogens, S. aureus and E. coli. Notably, the CRM system has the unique ability to provide Gram-staining classification and AST results within ~3 h directly from urine samples and shows great potential for clinical applications.
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Affiliation(s)
- Weifeng Zhang
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Hongyi Sun
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Shipei He
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
| | - Xun Chen
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- School of Engineering Medicine, Beihang University, Beijing, China
| | - Lin Yao
- Department of Urology, Peking University First Hospital, Beijing, China
- Lin Yao,
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Yi Wang
- Department of Clinical Laboratory, China Rehabilitation Research Center, Capital Medical University, Beijing, China
| | - Pu Wang
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- *Correspondence: Pu Wang,
| | - Weili Hong
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- Weili Hong,
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Chakrapani G, Zare M, Ramakrishna S. Current Trends and Definitions in High-performance Antimicrobial Strategies. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2022. [DOI: 10.1016/j.cobme.2022.100407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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57
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Mulroney K, Kopczyk M, Carson C, Paton T, Inglis T, Chakera A. Same-day confirmation of infection and antimicrobial susceptibility profiling using flow cytometry. EBioMedicine 2022; 82:104145. [PMID: 35864063 PMCID: PMC9386725 DOI: 10.1016/j.ebiom.2022.104145] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/21/2022] [Accepted: 06/21/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Kieran Mulroney
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia; School of Medicine, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
| | - Margaret Kopczyk
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia
| | - Christine Carson
- School of Biomedical Science, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; PathWest Laboratory Medicine WA, PP Block, QEII Medical Centre, Hospital Avenue, Nedlands, WA 6009, Australia
| | - Teagan Paton
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia; PathWest Laboratory Medicine WA, PP Block, QEII Medical Centre, Hospital Avenue, Nedlands, WA 6009, Australia
| | - Timothy Inglis
- School of Medicine, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; School of Biomedical Science, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; PathWest Laboratory Medicine WA, PP Block, QEII Medical Centre, Hospital Avenue, Nedlands, WA 6009, Australia
| | - Aron Chakera
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia; School of Medicine, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; Department of Renal Medicine, Sir Charles Gairdner Hospital, QEII Medical Centre, Hospital Avenue, Nedlands, WA 6009, Australia.
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58
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Muurinen J, Cairns J, Ekakoro JE, Wickware CL, Ruple A, Johnson TA. Biological units of antimicrobial resistance and strategies for their containment in animal production. FEMS Microbiol Ecol 2022; 98:6589402. [PMID: 35587376 DOI: 10.1093/femsec/fiac060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 05/27/2022] [Indexed: 11/14/2022] Open
Abstract
The increasing prevalence of antimicrobial resistant bacterial infections has ushered in a major global public health crisis. Judicious or restricted antimicrobial use in animal agriculture, aiming to confine the use for the treatment of infections, is the most commonly proposed solution to reduce selection pressure for resistant bacterial strains and resistance genes. However, a multifaceted solution will likely be required to make acceptable progress in reducing antimicrobial resistance, due to other common environmental conditions maintaining antimicrobial resistance and limited executionary potential as human healthcare and agriculture will continue to rely heavily on antimicrobials in the foreseeable future. Drawing parallels from systematic approaches to the management of infectious disease agents and biodiversity loss, we provide examples that a more comprehensive approach is required, targeting antimicrobial resistance in agroecosystems on multiple fronts simultaneously. We present one such framework, based on nested biological units of antimicrobial resistance, and describe established or innovative strategies targeting units. Some of the proposed strategies are already in use or ready to be implemented, while some require further research and discussion among scientists and policymakers. We envision that antimicrobial resistance mitigation strategies for animal agriculture combining multiple tools would constitute powerful ecosystem-level interventions necessary to mitigate antimicrobial resistance.
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Affiliation(s)
- Johanna Muurinen
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.,Department of Microbiology, Viikinkaari 9, 00014 University of Helsinki, Helsinki, Finland
| | - Johannes Cairns
- Organismal and Evolutionary Biology Research Programme (OEB), Department of Computer Science, 00014 University of Helsinki, Helsinki, Finland
| | - John Eddie Ekakoro
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Carmen L Wickware
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Audrey Ruple
- Department of Population Health Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Timothy A Johnson
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
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59
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Gao X, Li M, Zhao M, Wang X, Wang S, Liu Y. Metabolism-Triggered Colorimetric Sensor Array for Fingerprinting and Antibiotic Susceptibility Testing of Bacteria. Anal Chem 2022; 94:6957-6966. [PMID: 35500293 DOI: 10.1021/acs.analchem.1c05006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rapid identification and antibiotic susceptibility testing (AST) of bacteria would help us to accurately identify the infectious sources as well as guide the use of antibiotics, which are crucial for improving the survival rate and antimicrobial resistance. Herein, a colorimetric sensor array for bacteria fingerprinting was constructed with d-amino acid (d-AA)-modified gold nanoparticles (AuNPs) as probes (Au/d-AA). Bacteria can metabolize the d-AA, triggering the aggregation of AuNPs. Making use of different metabolic capabilities of bacteria toward different d-AA, eight kinds of bacteria including antibiotic-resistant bacteria and strains of the same bacterial species are successfully differentiated via learning the response patterns. Meanwhile, the sensor array also performs well in quantitative analysis of single bacterium and differentiation of bacteria mixtures. More interestingly, a rapid colorimetric AST approach has been developed based on the Au/d-AA nanoprobes by monitoring the d-AA metabolic activity of bacteria toward various antibiotic treatments. In this regard, the outlined work here would promote clinical practicability and facilitate antibiotic stewardship.
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Affiliation(s)
- Xia Gao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Miaomiao Li
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Minyang Zhao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Xinke Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Yaqing Liu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, P. R. China
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60
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Zhang W, Chen X, Zhang J, Chen X, Zhou L, Wang P, Hong W. Rapid antimicrobial susceptibility testing for mixed bacterial infection in urine by AI-stimulated Raman scattering metabolic imaging. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2022. [DOI: 10.1016/j.medntd.2022.100132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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61
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Rajaonison A, Le Page S, Maurin T, Chaudet H, Raoult D, Baron SA, Rolain JM. Antilogic, a new supervised machine learning software for the automatic interpretation of antibiotic susceptibility testing in clinical microbiology: proof-of-concept on three frequently isolated bacterial species. Clin Microbiol Infect 2022; 28:1286.e1-1286.e8. [DOI: 10.1016/j.cmi.2022.03.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 03/17/2022] [Accepted: 03/26/2022] [Indexed: 11/03/2022]
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63
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Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods. Antibiotics (Basel) 2022; 11:antibiotics11040427. [PMID: 35453179 PMCID: PMC9024665 DOI: 10.3390/antibiotics11040427] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Antimicrobial resistance (AMR) has emerged as a major threat to public health globally. Accurate and rapid detection of resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment, combined with antimicrobial stewardship, are essential for controlling the emergence and spread of AMR. This article reviews common antimicrobial susceptibility testing (AST) methods and relevant issues concerning the advantages and disadvantages of each method. Although accurate, classic technologies used in clinical microbiology to profile antimicrobial susceptibility are time-consuming and relatively expensive. As a result, physicians often prescribe empirical antimicrobial therapies and broad-spectrum antibiotics. Although recently developed AST systems have shown advantages over traditional methods in terms of testing speed and the potential for providing a deeper insight into resistance mechanisms, extensive validation is required to translate these methodologies to clinical practice. With a continuous increase in antimicrobial resistance, additional efforts are needed to develop innovative, rapid, accurate, and portable diagnostic tools for AST. The wide implementation of novel devices would enable the identification of the optimal treatment approaches and the surveillance of antibiotic resistance in health, agriculture, and the environment, allowing monitoring and better tackling the emergence of AMR.
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64
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Gu J, Song P, Chen X, Yang Z, Zhang X, Bai Y. Comparative study of the bacterial distribution and antimicrobial susceptibility of uropathogens in older and younger patients with urinary stones. BMC Geriatr 2022; 22:195. [PMID: 35279077 PMCID: PMC8918295 DOI: 10.1186/s12877-022-02886-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/24/2022] [Indexed: 11/26/2022] Open
Abstract
Background This study compared the bacterial spectrum and antibiotic susceptibility of uropathogens in older and younger patients with urinary stones to provide appropriate antibiotic management. Methods We retrospectively reviewed urinary tract infection patients with urolithiasis, presented to Xiangya Hospital from March 2014 to April 2021. Patients were divided into older and younger groups according to 60 years of age. The bacterial spectrum and drug sensitivity of uropathogens were compared. Results A total of 542 strains of uropathogens (177 in older and 365 in younger groups) were isolated from 507 patients. E. coli (41.8% vs 43.6%) remains the most common pathogen, followed by E. faecalis (6.2% vs 9.6%) in older and younger groups, respectively. Particularly, K. pneumoniae was significantly more frequent in older (9.6%) than in younger group (4.7%, P < .05). E. faecium was substantially more prevalent in older group (6.2%) than in younger group (2.7%, P < .05). The proportion of males increased in older patients (47.3%) than in younger patients (34.9%, P = 0.007). In both groups, major Gram-negative bacteria (E. coli and K. pneumoniae) revealed a high sensitivity over 70% to piperacillin/tazobactam, imipenem and amikacin, whereas the resistance level was high to penicillin, tetracycline and vancomycin. Major Gram-positive (E. faecalis and E. faecium) isolates demonstrated high sensitivity of over 50% to gentamicin and vancomycin in both groups. Furthermore, uropathogens isolated from younger urolithiasis patients were more susceptible to antimicrobials than those isolated from older patients. Conclusions The male increased in the older urolithiasis patients with UTI and uropathogens microbial spectrum in older urolithiasis patients are different from younger. High susceptibility and age should be utilized in empirical antibiotic selection to avoid increased multidrug-resistant bacteria.
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65
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A Review of Raman-Based Technologies for Bacterial Identification and Antimicrobial Susceptibility Testing. PHOTONICS 2022. [DOI: 10.3390/photonics9030133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Antimicrobial resistance (AMR) is a global medical threat that seriously endangers human health. Rapid bacterial identification and antimicrobial susceptibility testing (AST) are key interventions to combat the spread and emergence of AMR. Although current clinical bacterial identification and AST provide comprehensive information, they are labor-intensive, complex, inaccurate, and slow (requiring several days, depending on the growth of pathogenic bacteria). Recently, Raman-based identification and AST technologies have played an increasingly important role in fighting AMR. This review summarizes major Raman-based techniques for bacterial identification and AST, including spontaneous Raman scattering, surface-enhanced Raman scattering (SERS), and coherent Raman scattering (CRS) imaging. Then, we discuss recent developments in rapid identification and AST methods based on Raman technology. Finally, we highlight the major challenges and potential future efforts to improve clinical outcomes through rapid bacterial identification and AST.
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66
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Zhang M, Seleem MN, Cheng JX. Rapid Antimicrobial Susceptibility Testing by Stimulated Raman Scattering Imaging of Deuterium Incorporation in a Single Bacterium. J Vis Exp 2022:10.3791/62398. [PMID: 35225259 PMCID: PMC9682461 DOI: 10.3791/62398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
To slow and prevent the spread of antimicrobial resistant infections, rapid antimicrobial susceptibility testing (AST) is in urgent need to quantitatively determine the antimicrobial effects on pathogens. It typically takes days to complete the AST by conventional methods based on the long-time culture, and they do not work directly for clinical samples. Here, we report a rapid AST method enabled by stimulated Raman scattering (SRS) imaging of deuterium oxide (D2O) metabolic incorporation. Metabolic incorporation of D2O into biomass and the metabolic activity inhibition upon exposure to antibiotics at the single bacterium level are monitored by SRS imaging. The single-cell metabolism inactivation concentration (SC-MIC) of bacteria upon exposure to antibiotics can be obtained after a total of 2.5 h of sample preparation and detection. Furthermore, this rapid AST method is directly applicable to bacterial samples in complex biological environments, such as urine or whole blood. SRS metabolic imaging of deuterium incorporation is transformative for rapid single-cell phenotypic AST in the clinic.
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Affiliation(s)
- Meng Zhang
- Department of Electrical and Computer Engineering, Boston University; Boston University Photonics Center, Boston University
| | - Mohamed N Seleem
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University
| | - Ji-Xin Cheng
- Department of Electrical and Computer Engineering, Boston University; Boston University Photonics Center, Boston University; Department of Biomedical Engineering, Boston University; Department of Chemistry, Boston University;
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Investigating Unfavorable Factors That Impede MALDI-TOF-Based AI in Predicting Antibiotic Resistance. Diagnostics (Basel) 2022; 12:diagnostics12020413. [PMID: 35204505 PMCID: PMC8871102 DOI: 10.3390/diagnostics12020413] [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: 01/03/2022] [Revised: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 02/05/2023] Open
Abstract
The combination of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) spectra data and artificial intelligence (AI) has been introduced for rapid prediction on antibiotic susceptibility testing (AST) of Staphylococcus aureus. Based on the AI predictive probability, cases with probabilities between the low and high cut-offs are defined as being in the “grey zone”. We aimed to investigate the underlying reasons of unconfident (grey zone) or wrong predictive AST. In total, 479 S. aureus isolates were collected and analyzed by MALDI-TOF, and AST prediction and standard AST were obtained in a tertiary medical center. The predictions were categorized as correct-prediction group, wrong-prediction group, and grey-zone group. We analyzed the association between the predictive results and the demographic data, spectral data, and strain types. For methicillin-resistant S. aureus (MRSA), a larger cefoxitin zone size was found in the wrong-prediction group. Multilocus sequence typing of the MRSA isolates in the grey-zone group revealed that uncommon strain types comprised 80%. Of the methicillin-susceptible S. aureus (MSSA) isolates in the grey-zone group, the majority (60%) comprised over 10 different strain types. In predicting AST based on MALDI-TOF AI, uncommon strains and high diversity contribute to suboptimal predictive performance.
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68
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Recent Developments in Phenotypic and Molecular Diagnostic Methods for Antimicrobial Resistance Detection in Staphylococcus aureus: A Narrative Review. Diagnostics (Basel) 2022; 12:diagnostics12010208. [PMID: 35054375 PMCID: PMC8774325 DOI: 10.3390/diagnostics12010208] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Staphylococcus aureus is an opportunistic pathogen responsible for a wide range of infections in humans, such as skin and soft tissue infections, pneumonia, food poisoning or sepsis. Historically, S. aureus was able to rapidly adapt to anti-staphylococcal antibiotics and become resistant to several classes of antibiotics. Today, methicillin-resistant S. aureus (MRSA) is a multidrug-resistant pathogen and is one of the most common bacteria responsible for hospital-acquired infections and outbreaks, in community settings as well. The rapid and accurate diagnosis of antimicrobial resistance in S. aureus is crucial to the early initiation of directed antibiotic therapy and to improve clinical outcomes for patients. In this narrative review, I provide an overview of recent phenotypic and molecular diagnostic methods for antimicrobial resistance detection in S. aureus, with a particular focus on MRSA detection. I consider methods for resistance detection in both clinical samples and isolated S. aureus cultures, along with a brief discussion of the advantages and the challenges of implementing such methods in routine diagnostics.
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OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1020-1026. [DOI: 10.1093/jac/dkac003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/02/2021] [Indexed: 11/14/2022] Open
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Bellali S, Haddad G, Iwaza R, Fontanini A, Hisada A, Ominami Y, Raoult D, Khalil JB. Antimicrobial susceptibility testing for Gram positive cocci towards vancomycin using scanning electron microscopy. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100154. [PMID: 35909629 PMCID: PMC9325908 DOI: 10.1016/j.crmicr.2022.100154] [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] [Indexed: 11/26/2022] Open
Abstract
SEM-based method can be applied for rapid phenotypic AST on Gram-positive cocci towards 2 vancomycin based on morphological changes 3. The ratio of septa as a marker of bacterial division and size of grape-like clusters enabled the 4 profiling of E. faecalis, E. faecium and S. aureus after brief incubation with vancomycin 5. SEM-AST strategy showed the feasibility of detecting antibiotic susceptibility or 6 resistance on Gram-positive cocci within one hour of exposition to vancomycin 7.
The rapid detection of resistant bacteria has become a challenge for microbiologists worldwide. Numerous pathogens that cause nosocomial infections are still being treated empirically and have developed resistance mechanisms against key antibiotics. Thus, one of the challenges for researchers has been to develop rapid antimicrobial susceptibility testing (AST) to detect resistant isolates, ensuring better antibiotic stewardship. In this study, we established a proof-of-concept for a new strategy of phenotypic AST on Gram-positive cocci towards vancomycin using scanning electron microscopy (SEM). Our study evaluated the profiling of Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus after brief incubation with vancomycin. Sixteen isolates were analysed aiming to detect ultrastructural modifications at set timepoints, comparing bacteria with and without vancomycin. After optimising slides preparation and micrographs acquisition, two analytical strategies were used. The high magnification micrographs served to analyse the division of cocci based on the ratio of septa, along with the bacterial size. Susceptible strains with vancomycin showed a reduced septa percentage and the average surface area was consequently double that of the controls. The resistant bacteria revealed multiple septa occurring at advanced timepoints. Low magnification micrographs made it possible to quantify the pixels at different timepoints, confirming the profiling of cocci towards vancomycin. This new phenotypic AST strategy proved to be a promising tool to discriminate between resistant and susceptible cocci within an hour of contact with vancomycin. The analysis strategies applied here would potentially allow the creation of artificial intelligence algorithms for septa detection and bacterial quantification, subsequently creating a rapid automated SEM-AST assay.
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71
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Wang X, Liu NM, Zhao YF, Yang F, Zhu ZJ, Song D. Research Progress in the Medical Application of Heavy Water, Especially in the Field of D 2O-Raman Spectroscopy. Int J Med Sci 2022; 19:1357-1363. [PMID: 35928718 PMCID: PMC9346379 DOI: 10.7150/ijms.73150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/07/2022] [Indexed: 11/05/2022] Open
Abstract
Heavy water is an ideal contrast agent for metabolic activity and can be adapted to a wide range of biological systems owing to its non-invasiveness, universal applicability, and cost-effectiveness. As a new type of probe, the heavy isotope of water has been widely used in the study of cell development, metabolism, tissue homeostasis, aging, and tumor heterogeneity. Herein, we review findings supporting the applications of and research on heavy water in monitoring of bacterial metabolism, rapid detection of drug sensitivity, identification of tumor cells, precision medicine, and evaluation of skin barrier function and promote the use of heavy water as a suitable marker for the development of detection and treatment methodologies.
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Affiliation(s)
- Xin Wang
- Department of Breast Surgery, First Hospital of Jilin University, Changchun, Jilin 130021
| | - Nai-Meng Liu
- Department of Breast Surgery, First Hospital of Jilin University, Changchun, Jilin 130021
| | - Ya-Fei Zhao
- Department of Breast Surgery, First Hospital of Jilin University, Changchun, Jilin 130021
| | - Fan Yang
- Department of Breast Surgery, First Hospital of Jilin University, Changchun, Jilin 130021
| | - Zi-Jia Zhu
- Department of Breast Surgery, First Hospital of Jilin University, Changchun, Jilin 130021
| | - Dong Song
- Department of Breast Surgery, First Hospital of Jilin University, Changchun, Jilin 130021
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Datar R, Orenga S, Pogorelcnik R, Rochas O, Simner PJ, van Belkum A. Recent Advances in Rapid Antimicrobial Susceptibility Testing. Clin Chem 2021; 68:91-98. [DOI: 10.1093/clinchem/hvab207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/17/2021] [Indexed: 12/30/2022]
Abstract
Abstract
Background
Antimicrobial susceptibility testing (AST) is classically performed using growth-based techniques that essentially require viable bacterial matter to become visible to the naked eye or a sophisticated densitometer.
Content
Technologies based on the measurement of bacterial density in suspension have evolved marginally in accuracy and rapidity over the 20th century, but assays expanded for new combinations of bacteria and antimicrobials have been automated, and made amenable to high-throughput turn-around. Over the past 25 years, elevated AST rapidity has been provided by nucleic acid-mediated amplification technologies, proteomic and other “omic” methodologies, and the use of next-generation sequencing. In rare cases, AST at the level of single-cell visualization was developed. This has not yet led to major changes in routine high-throughput clinical microbiological detection of antimicrobial resistance.
Summary
We here present a review of the new generation of methods and describe what is still urgently needed for their implementation in day-to-day management of the treatment of infectious diseases.
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Affiliation(s)
- Rucha Datar
- bioMérieux, Microbiology Research, La Balme Les Grottes, France
| | - Sylvain Orenga
- bioMérieux, Microbiology Research, La Balme Les Grottes, France
| | | | - Olivier Rochas
- bioMérieux, Corporate Business Development, Marcy l'Etoile, France
| | - Patricia J Simner
- Department of Pathology, Bacteriology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, La Balme Les Grottes, France
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Fitzpatrick KJ, Rohlf HJ, Sutherland TD, Koo KM, Beckett S, Okelo WO, Keyburn AL, Morgan BS, Drigo B, Trau M, Donner E, Djordjevic SP, De Barro PJ. Progressing Antimicrobial Resistance Sensing Technologies across Human, Animal, and Environmental Health Domains. ACS Sens 2021; 6:4283-4296. [PMID: 34874700 DOI: 10.1021/acssensors.1c01973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The spread of antimicrobial resistance (AMR) is a rapidly growing threat to humankind on both regional and global scales. As countries worldwide prepare to embrace a One Health approach to AMR management, which is one that recognizes the interconnectivity between human, animal, and environmental health, increasing attention is being paid to identifying and monitoring key contributing factors and critical control points. Presently, AMR sensing technologies have significantly progressed phenotypic antimicrobial susceptibility testing (AST) and genotypic antimicrobial resistance gene (ARG) detection in human healthcare. For effective AMR management, an evolution of innovative sensing technologies is needed for tackling the unique challenges of interconnected AMR across various and different health domains. This review comprehensively discusses the modern state-of-play for innovative commercial and emerging AMR sensing technologies, including sequencing, microfluidic, and miniaturized point-of-need platforms. With a unique view toward the future of One Health, we also provide our perspectives and outlook on the constantly changing landscape of AMR sensing technologies beyond the human health domain.
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Affiliation(s)
- Kira J. Fitzpatrick
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
| | - Hayden J. Rohlf
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
| | - Tara D. Sutherland
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Kevin M. Koo
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty. Ltd., Brisbane, Queensland 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, Queensland 4029, Australia
| | - Sam Beckett
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Walter O. Okelo
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Anthony L. Keyburn
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness (ACDP), Geelong, Victoria 3220, Australia
| | - Branwen S. Morgan
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Black Mountain, Canberra, Australian Capital Territory 2601, Australia
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, South Australia 5095, Australia
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, South Australia 5095, Australia
| | - Steven P. Djordjevic
- Ithree Institute, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Paul J. De Barro
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Health & Biosecurity, EcoSciences Precinct, Brisbane, Queensland 4001, Australia
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Scaglione V, Reale M, Davoli C, Mazzitelli M, Serapide F, Lionello R, La Gamba V, Fusco P, Bruni A, Procopio D, Garofalo E, Longhini F, Marascio N, Peronace C, Giancotti A, Gallo L, Matera G, Liberto MC, Cesana BM, Costa C, Trecarichi EM, Quirino A, Torti C. Prevalence of Antibiotic Resistance Over Time in a Third-Level University Hospital. Microb Drug Resist 2021; 28:425-435. [PMID: 34910885 PMCID: PMC9058886 DOI: 10.1089/mdr.2021.0109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This study evaluated the spread and possible changes in resistance patterns of ESKAPE bacteria to first-choice antibiotics from 2015 to 2019 at a third-level university hospital after persuasive stewardship measures were implemented. Isolates were divided into three groups (group 1, low drug-resistant; group 2, multidrug/extremely drug-resistant; and group 3, pan-resistant bacteria) and a chi-squared test (χ2) was applied to determine differences in their distributions. Among the 2,521 isolates, Klebsiella pneumoniae was the most frequently detected (31.1%). From 2015 to 2019, the frequency of isolates in groups 2 and 3 decreased from 70.1% to 48.6% (χ2 = 63.439; p < 0.0001). Stratifying isolates by bacterial species, for K. pneumoniae, the frequency of PDR isolates decreased from 20% to 1.3% (χ2 = 15.885; p = 0.003). For Acinetobacter baumannii, a statistically significant decrease was found in groups 2 and 3: from 100% to 83.3% (χ2 = 27.721; p < 0.001). Also, for Pseudomonas aeruginosa and Enterobacter spp., the frequency of groups 2 and 3 decreased from 100% to 28.3% (χ2 = 225.287; p < 0.001) and from 75% to 48.7% (χ2 = 15.408; p = 0.003), respectively. These results indicate that a program consisting of persuasive stewardship measures, which were rolled out during the time frame of our study, may be useful to control drug-resistant bacteria in a hospital setting.
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Affiliation(s)
- Vincenzo Scaglione
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Mariaconcetta Reale
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Chiara Davoli
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Maria Mazzitelli
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Francesca Serapide
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Rosaria Lionello
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Valentina La Gamba
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Paolo Fusco
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Andrea Bruni
- Unit of Intensive Care, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Daniela Procopio
- Unit of Intensive Care, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Eugenio Garofalo
- Unit of Intensive Care, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Federico Longhini
- Unit of Intensive Care, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Nadia Marascio
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Cinzia Peronace
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Aida Giancotti
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Luigia Gallo
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Giovanni Matera
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Maria Carla Liberto
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Bruno Mario Cesana
- Unit of Medical Statistics, Biometrics and Bioinformatics "Giulio A. Maccacaro", Department of Clinical Sciences and Community Health, Faculty of Medicine and Surgery, University of Milan, Milan, Italy
| | - Chiara Costa
- Unit of Infectious and Tropical Diseases, "Mater Domini" Teaching Hospital, Catanzaro, Italy
| | - Enrico Maria Trecarichi
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Angela Quirino
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Carlo Torti
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
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Gu J, Chen X, Yang Z, Bai Y, Zhang X. Gender differences in the microbial spectrum and antibiotic sensitivity of uropathogens isolated from patients with urinary stones. J Clin Lab Anal 2021; 36:e24155. [PMID: 34854120 PMCID: PMC8761408 DOI: 10.1002/jcla.24155] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/19/2021] [Accepted: 11/20/2021] [Indexed: 11/18/2022] Open
Abstract
Purpose The characteristics and resistance patterns of urine bacteriology urolithiasis patients between male and female have not been extensively studied. This study aims to investigate the gender differences in microbial spectrum and antibiotic susceptibility of uropathogens isolated from urolithiasis patients and provide insights for appropriate antimicrobial therapies. Materials and Methods We retrospectively collected clinical microbiology data from urine culture in urolithiasis patients between March 2014 and December 2018 in Xiangya Hospital. Then the patients were divided into male and female groups. The microbial spectrum and frequency of susceptibility to antibiotics were compared. Results A total of 359 uropathogen isolates were collected from 335 patients, including 144 males (43.0%) and 191 females (57.0%). E. coli dominated in both groups, indicating higher frequency in females (53.2%) than in males (26.6%, p < 0.001), followed by E. faecalis, with higher frequency in males (15.6%) than in females (2.9%, p < 0.001). Major Gram‐negative (E. coli and K. pneumoniae) bacteria showed high sensitivity to cefoperazone/sulbactam, cefotetan, piperacillin/ tazobactam, and amikacin. In contrast, the resistance level was high to penicillin, tetracycline, and vancomycin in both groups. Gram‐positive (E. faecalis and E. faecium) isolates demonstrated high sensitivity to gentamicin and vancomycin in both groups. Furthermore, uropathogens isolated from female urolithiasis patients were more susceptible to antimicrobials than males. Conclusions Uropathogen microbial spectrum in female urolithiasis patients is different from males. High susceptibility antibiotics should be used empirically according to gender to avoid multidrug‐resistant bacteria increase.
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Affiliation(s)
- Jie Gu
- Department of Geriatric Urology, Xiangya International Medical Center, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Martini-Klinik Prostate Cancer Center, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Xiong Chen
- Department of Geriatric Urology, Xiangya International Medical Center, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhiming Yang
- Department of Geriatric Urology, Xiangya International Medical Center, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yao Bai
- Department of Urology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Xiaobo Zhang
- Department of Geriatric Urology, Xiangya International Medical Center, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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Lu J, Chen J, Liu C, Zeng Y, Sun Q, Li J, Shen Z, Chen S, Zhang R. Identification of antibiotic resistance and virulence-encoding factors in Klebsiella pneumoniae by Raman spectroscopy and deep learning. Microb Biotechnol 2021; 15:1270-1280. [PMID: 34843635 PMCID: PMC8966003 DOI: 10.1111/1751-7915.13960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
Klebsiella pneumoniae has become the number one bacterial pathogen that causes high mortality in clinical settings worldwide. Clinical K. pneumoniae strains with carbapenem resistance and/or hypervirulent phenotypes cause higher mortality comparing with classical K. pneumoniae strains. Rapid differentiation of clinical K. pneumoniae with high resistance/hypervirulence from classical K. pneumoniae would allow us to develop rational and timely treatment plans. In this study, we developed a convolution neural network (CNN) as a prediction method using Raman spectra raw data for rapid identification of ARGs, hypervirulence‐encoding factors and resistance phenotypes from K. pneumoniae strains. A total of 71 K. pneumoniae strains were included in this study. The minimum inhibitory concentrations (MICs) of 15 commonly used antimicrobial agents on K. pneumoniae strains were determined. Seven thousand four hundred fifty‐five spectra were obtained using the InVia Reflex confocal Raman microscope and used for deep learning‐based and machine learning (ML) algorithms analyses. The quality of predictors was estimated in an independent data set. The results of antibiotic resistance and virulence‐encoding factors identification showed that the CNN model not only simplified the classification system for Raman spectroscopy but also provided significantly higher accuracy to identify K. pneumoniae with high resistance and virulence when compared with the support vector machine (SVM) and logistic regression (LR) models. By back‐testing the Raman‐CNN platform on 71 K. pneumoniae strains, we found that Raman spectroscopy allows for highly accurate and rationally designed treatment plans against bacterial infections within hours. More importantly, this method could reduce healthcare costs and antibiotics misuse, limiting the development of antimicrobial resistance and improving patient outcomes.
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Affiliation(s)
- Jiayue Lu
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jifan Chen
- Department of Ultrasound, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Congcong Liu
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Zeng
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiaoling Sun
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiaping Li
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhangqi Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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77
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Tang H, Li R, Xu H, Lu G, Liu Z, Yang W, Xia Z, Zhu Y, Shen J. Direct-on-Target Microdroplet Growth Assay for Detection of Bacterial Resistance in Positive Blood Cultures. Infect Drug Resist 2021; 14:4611-4617. [PMID: 34785912 PMCID: PMC8579891 DOI: 10.2147/idr.s336987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/28/2021] [Indexed: 12/17/2022] Open
Abstract
Introduction The recently developed DOT-MGA (direct-on-target microdroplet growth assay) has shown the desirability of direct application of this approach in positive blood cultures and its good performance in detection. This study selected 44 Enterobacteriaceae strains and implemented a DOT-MGA assay on blood cultures to detect their resistance to seven antibiotics. The results of DOT-MGA were compared with the other two antimicrobial susceptibility testing (AST) methods to analyze the detection performance of DOT-MGA. Methods We adopted the differential centrifugation to process positive blood-culture (BC). Processed BC broth was directly used for rapid AST using DOT-MGA. Droplets of 6 µL with and without antibiotics at the EUCAST breakpoint concentration were spotted in triplicates onto the surface of a MALDI target. The plates were incubated in a wet box for 4 h before the broth was removed with filter paper. Bruker Biotyper software was used to analyze the test results compared with standard database, and the scores were used to quantify and determine the results. Results DOT-MGA results were compared with the direct-from-BC disk-diffusion method and results were reported by broth microdilution method, respectively. The comparison demonstrated a 100% growth efficiency in DOT-MGA, a 100% classification consistency for ampicillin, ceftriaxone, and gentamicin, and >93% classification consistency for tobramycin, aztreonam, trimethoprim-sulfamethoxazole (TMP-SMX), and ceftazidime. Discussion These study results have shown that DOT-MGA is suitable for directly identifying bacterial resistance to positive blood cultures in clinical microbiology laboratories. Furthermore, it is conducive for early diagnosis and treatment of patients with bloodstream infection due to its convenience, time efficiency, and good performance in identifying multiple antibiotic-insensitive bacteria.
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Affiliation(s)
- Hao Tang
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People's Republic of China
| | - Rongrong Li
- The First Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People's Republic of China
| | - Huaming Xu
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People's Republic of China
| | - Guoping Lu
- Laboratory Department of Fuyang Hospital Affiliated to Anhui Medical University, Fuyang, Anhui, 236000, People's Republic of China
| | - Zhen Liu
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People's Republic of China
| | - Wensu Yang
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People's Republic of China
| | - Zhaoxin Xia
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People's Republic of China
| | - Yi Zhu
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People's Republic of China
| | - Jilu Shen
- The Fourth Affiliated Hospital of Anhui Medical University Laboratory Department, Hefei, People's Republic of China
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He S, Leanse LG, Feng Y. Artificial intelligence and machine learning assisted drug delivery for effective treatment of infectious diseases. Adv Drug Deliv Rev 2021; 178:113922. [PMID: 34461198 DOI: 10.1016/j.addr.2021.113922] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/14/2021] [Accepted: 08/09/2021] [Indexed: 12/23/2022]
Abstract
In the era of antimicrobial resistance, the prevalence of multidrug-resistant microorganisms that resist conventional antibiotic treatment has steadily increased. Thus, it is now unquestionable that infectious diseases are significant global burdens that urgently require innovative treatment strategies. Emerging studies have demonstrated that artificial intelligence (AI) can transform drug delivery to promote effective treatment of infectious diseases. In this review, we propose to evaluate the significance, essential principles, and popular tools of AI in drug delivery for infectious disease treatment. Specifically, we will focus on the achievements and key findings of current research, as well as the applications of AI on drug delivery throughout the whole antimicrobial treatment process, with an emphasis on drug development, treatment regimen optimization, drug delivery system and administration route design, and drug delivery outcome prediction. To that end, the challenges of AI in drug delivery for infectious disease treatments and their current solutions and future perspective will be presented and discussed.
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Affiliation(s)
- Sheng He
- Boston Children's Hospital, Harvard Medical School, Harvard University, Boston, MA, USA.
| | - Leon G Leanse
- Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Yanfang Feng
- Massachusetts General Hospital, Harvard Medical School, Harvard University, Boston, MA, USA.
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Heuer C, Bahnemann J, Scheper T, Segal E. Paving the Way to Overcome Antifungal Drug Resistance: Current Practices and Novel Developments for Rapid and Reliable Antifungal Susceptibility Testing. SMALL METHODS 2021; 5:e2100713. [PMID: 34927979 DOI: 10.1002/smtd.202100713] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/05/2021] [Indexed: 06/14/2023]
Abstract
The past year has established the link between the COVID-19 pandemic and the global spread of severe fungal infections; thus, underscoring the critical need for rapid and realizable fungal disease diagnostics. While in recent years, health authorities, such as the Centers for Disease Control and Prevention, have reported the alarming emergence and spread of drug-resistant pathogenic fungi and warned against the devastating consequences, progress in the diagnosis and treatment of fungal infections is limited. Early diagnosis and patient-tailored therapy are established to be key in reducing morbidity and mortality associated with fungal (and cofungal) infections. As such, antifungal susceptibility testing (AFST) is crucial in revealing susceptibility or resistance of these pathogens and initiating correct antifungal therapy. Today, gold standard AFST methods require several days for completion, and thus this much delayed time for answer limits their clinical application. This review focuses on the advancements made in developing novel AFST techniques and discusses their implications in the context of the practiced clinical workflow. The aim of this work is to highlight the advantages and drawbacks of currently available methods and identify the main gaps hindering their progress toward clinical application.
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Affiliation(s)
- Christopher Heuer
- Institute of Technical Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 320003, Israel
| | - Janina Bahnemann
- Institute of Technical Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University Hannover, 30167, Hannover, Germany
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 320003, Israel
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80
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Mishra R, Chaurasia H, Singh VK, Naaz F, Singh RK. Molecular modeling, QSAR analysis and antimicrobial properties of Schiff base derivatives of isatin. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130763] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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81
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Suwono B, Hammerl JA, Eckmanns T, Merle R, Eigner U, Lümen M, Lauter S, Stock R, Fenner I, Boemke E, Tenhagen BA. Comparison of MICs in Escherichia coli isolates from human health surveillance with MICs obtained for the same isolates by broth microdilution. JAC Antimicrob Resist 2021; 3:dlab145. [PMID: 34676365 PMCID: PMC8524623 DOI: 10.1093/jacamr/dlab145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 08/11/2021] [Indexed: 11/14/2022] Open
Abstract
Objectives Human health surveillance and food safety monitoring systems use different antimicrobial susceptibility testing (AST) methods. In this study, we compared the MICs of Escherichia coli isolates provided by these methods. Methods E. coli isolates (n = 120) from human urine samples and their MICs were collected from six medical laboratories that used automated AST methods based on bacterial growth kinetic analyses. These isolates were retested using broth microdilution, which is used by the food safety monitoring system. The essential and categorical agreements (EA and CA), very major errors (VME), major errors (ME) and minor errors (mE) for these two methods were calculated for 11 antibiotics using broth microdilution as a reference. For statistical analysis, clinical breakpoints provided by EUCAST were used. Results Five study laboratories used VITEK®2 and one MicroScan (Walkaway Combo Panel). Out of 120 isolates, 118 isolates (98.3%) were confirmed as E. coli. The 99 E. coli isolates from five study laboratories that used VITEK®2 showed high proportions of EA and CA with full agreements for gentamicin, meropenem, imipenem and ertapenem. Additionally, 100% CA was also observed in cefepime. Few VME (0.5%), ME (1.9%) and mE (1.5%) were observed across all antibiotics. One VME for ceftazidime (7.1%) and 12 MEs for ampicillin (29.4%), cefotaxime (2.4%), ciprofloxacin (3.2%), tigecycline (1.5%) and trimethoprim (22.2%) were detected. Conclusions MICs from E. coli isolates produced by VITEK®2 were similar to those determined by broth microdilution. These results will be valuable for comparative analyses of resistance data from human health surveillance and food safety monitoring systems.
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Affiliation(s)
- Beneditta Suwono
- Unit Epidemiology, Zoonoses and Antimicrobial Resistance, Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany.,Division of Healthcare-associated Infections, Surveillance of Antibiotic Resistance and Consumption, Department Infectious of Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Jens André Hammerl
- Unit Epidemiology, Zoonoses and Antimicrobial Resistance, Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Tim Eckmanns
- Division of Healthcare-associated Infections, Surveillance of Antibiotic Resistance and Consumption, Department Infectious of Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Roswitha Merle
- Department of Veterinary Medicine, Institute for Veterinary Epidemiology and Biostatistics, Free University Berlin, Berlin, Germany
| | - Ulrich Eigner
- Study Department for Infectious Diseases, MVZ Labor Dr. Limbach & Kollegen GbR, Heidelberg, Germany
| | - Michaela Lümen
- Department of Microbiology, Labor Mönchengladbach MVZ Dr Stein + Kollegen DbR, Mönchengladbach, Germany
| | - Sven Lauter
- Department of Bacteriology, LADR GmbH MVZ Nord, Flintbek, Germany
| | - Rüdiger Stock
- Department of Microbiology, SYNLAB MVZ Berlin GmbH, Berlin, Germany
| | - Ines Fenner
- Labor Dr. Fenner & Kollegen MVZ, Hamburg, Germany
| | - Eva Boemke
- Zentrallabor FEK-Friedrich-Ebert-Krankenhaus Neumünster GmbH, Neumünster, Germany
| | - Bernd-Alois Tenhagen
- Unit Epidemiology, Zoonoses and Antimicrobial Resistance, Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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82
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Liu Y, Lehnert T, Gijs MAM. Effect of inoculum size and antibiotics on bacterial traveling bands in a thin microchannel defined by optical adhesive. MICROSYSTEMS & NANOENGINEERING 2021; 7:86. [PMID: 34745645 PMCID: PMC8536744 DOI: 10.1038/s41378-021-00309-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Phenotypic diversity in bacterial flagella-induced motility leads to complex collective swimming patterns, appearing as traveling bands with transient locally enhanced cell densities. Traveling bands are known to be a bacterial chemotactic response to self-generated nutrient gradients during growth in resource-limited microenvironments. In this work, we studied different parameters of Escherichia coli (E. coli) collective migration, in particular the quantity of bacteria introduced initially in a microfluidic chip (inoculum size) and their exposure to antibiotics (ampicillin, ciprofloxacin, and gentamicin). We developed a hybrid polymer-glass chip with an intermediate optical adhesive layer featuring the microfluidic channel, enabling high-content imaging of the migration dynamics in a single bacterial layer, i.e., bacteria are confined in a quasi-2D space that is fully observable with a high-magnification microscope objective. On-chip bacterial motility and traveling band analysis was performed based on individual bacterial trajectories by means of custom-developed algorithms. Quantifications of swimming speed, tumble bias and effective diffusion properties allowed the assessment of phenotypic heterogeneity, resulting in variations in transient cell density distributions and swimming performance. We found that incubation of isogeneic E. coli with different inoculum sizes eventually generated different swimming phenotype distributions. Interestingly, incubation with antimicrobials promoted bacterial chemotaxis in specific cases, despite growth inhibition. Moreover, E. coli filamentation in the presence of antibiotics was assessed, and the impact on motility was evaluated. We propose that the observation of traveling bands can be explored as an alternative for fast antimicrobial susceptibility testing.
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Affiliation(s)
- Yang Liu
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas Lehnert
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Martin A. M. Gijs
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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83
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Abstract
PURPOSE OF REVIEW Staphylococcus aureus is the most common invasive bacterial pathogen infecting children in the U.S. and many parts of the world. This major human pathogen continues to evolve, and recognition of recent trends in epidemiology, therapeutics and future horizons is of high importance. RECENT FINDINGS Over the past decade, a relative rise of methicillin-susceptible S. aureus (MSSA) has occurred, such that methicillin-resistant S. aureus (MRSA) no longer dominates the landscape of invasive disease. Antimicrobial resistance continues to develop, however, and novel therapeutics or preventive modalities are urgently needed. Unfortunately, several recent vaccine attempts proved unsuccessful in humans. SUMMARY Recent scientific breakthroughs highlight the opportunity for novel interventions against S. aureus by interfering with virulence rather than by traditional antimicrobial mechanisms. A S. aureus vaccine remains elusive; the reasons for this are multifactorial, and lessons learned from prior unsuccessful attempts may create a path toward an effective preventive. Finally, new diagnostic modalities have the potential to greatly enhance clinical care for invasive S. aureus disease in children.
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Affiliation(s)
- James E. Cassat
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation (VI4), Nashville, Tennessee, USA
- Vanderbilt Center for Bone Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Isaac Thomsen
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation (VI4), Nashville, Tennessee, USA
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84
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Idelevich EA, Nix ID, Busch JA, Sparbier K, Drews O, Kostrzewa M, Becker K. Rapid Simultaneous Testing of Multiple Antibiotics by the MALDI-TOF MS Direct-on-Target Microdroplet Growth Assay. Diagnostics (Basel) 2021; 11:diagnostics11101803. [PMID: 34679499 PMCID: PMC8534412 DOI: 10.3390/diagnostics11101803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022] Open
Abstract
Accelerating antimicrobial susceptibility testing (AST) is a priority in the development of novel microbiological methods. The MALDI-TOF MS-based direct-on-target microdroplet growth assay (DOT-MGA) has recently been described as a rapid phenotypic AST method. In this proof-of-principle study, we expanded this method to simultaneously test 24 antimicrobials. An Enterobacterales panel was designed and evaluated using 24 clinical isolates. Either one or two (only for antimicrobials with the EUCAST “I” category) breakpoint concentrations were tested. Microdroplets containing bacterial suspensions with antimicrobials and growth controls were incubated directly on the spots of a disposable MALDI target inside a humidity chamber for 6, 8 or 18 h. Broth microdilution was used as the standard method. After 6 and 8 h of incubation, the testing was valid (i.e., growth control was successfully detected) for all isolates and the overall categorical agreement was 92.0% and 92.7%, respectively. Although the overall assay performance applying short incubation times is promising, the lower performance with some antimicrobials and when using the standard incubation time of 18 h indicates the need for thorough standardization of assay conditions. While using “homebrew” utensils and provisional evaluation algorithms here, technical solutions such as dedicated incubation chambers, tools for broth removal and improved software analyses are needed.
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Affiliation(s)
- Evgeny A. Idelevich
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany;
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (I.D.N.); (J.A.B.)
| | - Ilka D. Nix
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (I.D.N.); (J.A.B.)
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany; (K.S.); (O.D.); (M.K.)
| | - Janika A. Busch
- Institute of Medical Microbiology, University Hospital Münster, 48149 Münster, Germany; (I.D.N.); (J.A.B.)
| | - Katrin Sparbier
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany; (K.S.); (O.D.); (M.K.)
| | - Oliver Drews
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany; (K.S.); (O.D.); (M.K.)
| | - Markus Kostrzewa
- Bruker Daltonics GmbH & Co. KG, 28359 Bremen, Germany; (K.S.); (O.D.); (M.K.)
| | - Karsten Becker
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany;
- Correspondence: ; Tel.: +49-3834-86-5560
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85
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Nicolai E, Pieri M, Gratton E, Motolese G, Bernardini S. Bacterial Infection Diagnosis and Antibiotic Prescription in 3 h as an Answer to Antibiotic Resistance: The Case of Urinary Tract Infections. Antibiotics (Basel) 2021; 10:antibiotics10101168. [PMID: 34680749 PMCID: PMC8532666 DOI: 10.3390/antibiotics10101168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/18/2021] [Accepted: 09/23/2021] [Indexed: 11/30/2022] Open
Abstract
Current methods for the diagnosis of urinary tract infections with antimicrobial susceptibility testing take 2–3 days and require a clinical laboratory. The lack of a rapid, point-of-care antibiotic susceptibility test (AST) has contributed to the misuse of antibiotics when treating urinary tract infections (UTIs) and consequently to the rise of multi-drug-resistant organisms. The current clinical approach has led to reduced treatment options and increased costs of diagnosis and therapy. To address this issue, novel diagnostics are needed for the timely determination of antimicrobial susceptibility. We present a rapid, point-of-care, phenotypic AST device that can report the antibiotic susceptibility/resistance of a uropathogen to a panel of antibiotics in as few as 3 h by utilizing fluorescent-labelling chemistry and a highly sensitive particle-counting instrument. We analysed 744 urine samples from the outpatients and inpatients of two Italian hospitals. The 130 UTI-positive patient urine samples we found were measured using a panel of six common UTI antibiotics plus a growth control. By comparing our results to hospital laboratory urine cultures, we obtained an overall sensitivity = 81%, a specificity = 83%, an SPV (sensitivity predicted value) = 95%, and an RPV (resistance predicted value) = 54%. According to our preliminary data, the sensitivity predicted value for a single antibiotic agent was 95%, thus allowing (in the vast majority of cases) an early (within 3 h) recognition of an effective agent for a single patient.
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Affiliation(s)
- Eleonora Nicolai
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.P.); (S.B.)
- Correspondence:
| | - Massimo Pieri
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.P.); (S.B.)
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California-Irvine, Irvine, CA 92697, USA;
| | | | - Sergio Bernardini
- Department of Experimental Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.P.); (S.B.)
- IFCC Emerging Technologies Divison, Via Carlo Farini 81, 20159 Milan, Italy
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86
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Chen J, Navarro E, Nuñez E, Gau V. Rapid Electrochemical-Based PCR-Less Microbial Quantification and Antimicrobial Susceptibility Profiling Directly From Blood and Urine With Unknown Microbial Load or Species. Front Bioeng Biotechnol 2021; 9:744198. [PMID: 34604191 PMCID: PMC8481646 DOI: 10.3389/fbioe.2021.744198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 08/30/2021] [Indexed: 11/30/2022] Open
Abstract
Novel molecular platforms are available for identifying (ID) the causative agents of microbial infections and generating antimicrobial susceptibility testing (AST) profiles, which can inform the suitable course of treatment. Many methods claim to perform AST in minutes or hours, often ignoring the need for time-consuming steps such as enrichment cultures and isolation of pure cultures. In clinical microbiology laboratories, an infectious microbial must first be cultured (overnight to days) and identified at the species level, followed by a subsequent AST with an additional turnaround time of 12-48 h due to the need for regrowth of the organism in the absence and presence of relevant antibiotics. Here, we present an electrochemical-based direct-from-specimen ID/AST method for reporting directly from unprocessed urine and blood in hours. In a limit of detection study of 0.5-ml whole blood samples for point-of-care and pediatric applications, 16.7% (4/24) of samples contrived at 2 CFU/ml and 100% (24/24) of samples contrived at 6 CFU/ml were reported positive in 6.5 h, indicating a limit of detection of 6 CFU/ml. In a separate direct-from-specimen AST study, the categorical susceptibility was reported correctly for blinded susceptible, intermediate, resistant, and polymicrobial contrived specimens in 4 h.
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87
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Liu Y, Lehnert T, Mayr T, Gijs MAM. Antimicrobial susceptibility testing by measuring bacterial oxygen consumption on an integrated platform. LAB ON A CHIP 2021; 21:3520-3531. [PMID: 34286790 DOI: 10.1039/d1lc00296a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cellular respiration is a fundamental feature of metabolic activity and oxygen consumption can be considered as a reliable indicator of bacterial aerobic respiration, including for facultative anaerobic bacteria like E. coli. Addressing the emerging global health challenge of antimicrobial resistance, we performed antimicrobial susceptibility testing using the bacterial oxygen consumption rate (OCR) as a phenotypic indicator. We demonstrated that microbial exposure to antibiotics showed systematic OCR variations, which enabled determining minimum inhibitory concentrations for three clinically relevant antibiotics, ampicillin, ciprofloxacin, and gentamicin, within a few hours. Our study was performed by using photoluminescence-based oxygen sensing in a microchamber format, which enabled reducing the sample volume to a few hundred microliters. OCR modeling based on exponential bacterial growth allowed estimating the bacterial doubling time for various culture conditions (different types of media, different culture temperature and antibiotic concentrations). Furthermore, correlating metabolic heat production data, as obtained by nanocalorimetry in the same type of microchamber, and OCR measurements provided further insight on the actual metabolic state and activity of a microbial sample. This approach represents a new path towards more comprehensive microbiological studies performed on integrated miniaturized systems.
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Affiliation(s)
- Yang Liu
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Thomas Lehnert
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Torsten Mayr
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, 80 Graz, Austria
| | - Martin A M Gijs
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
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Sharma M, Gangakhedkar RR, Bhattacharya S, Walia K. Understanding complexities in the uptake of indigenously developed rapid point-of-care diagnostics for containment of antimicrobial resistance in India. BMJ Glob Health 2021; 6:e006628. [PMID: 34580070 PMCID: PMC8477250 DOI: 10.1136/bmjgh-2021-006628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/19/2021] [Indexed: 11/21/2022] Open
Abstract
A good point-of-care diagnostic test holds a promise to reduce inappropriate use of antibiotics by enabling early detection of the pathogen and facilitating rapid testing of antimicrobial susceptibility. India has taken many initiatives in the recent past to augment the development and deployment of diagnostics in Indian health care system. Funding opportunities to promote innovation in diagnostics development were started in early 2000s through various ministries and departments. India released National Essential Diagnostics List which enlists essential tests and there is now Free Diagnostics Service Initiative of Government of India under National Health Mission that mandates to provide all essential tests free of cost. We wanted to understand how these initiatives have impacted the diagnostics that could be of use in containment of antimicrobial resistance (AMR) and whether there is a smooth process for bringing indigenously developed products relevant to AMR into the healthcare system. We conducted a longitudinal survey (January 2019 and January 2021) to understand the availability of market ready indigenous rapid diagnostics for AMR in the country and their progress towards introduction in the private market or uptake in healthcare system. We found that many innovators and developers are working towards development of rapid tests that can be useful in the containment of AMR in India. While there are many promising diagnostics on the horizon, the pathway for uptake of indigenously developed diagnostics in healthcare system remains disjointed and needs to be harmonised for the investments made towards development to translate as tangible gains. Since most of these efforts are government funded, it is incumbent upon the government to also provide a seamless pathway to make these diagnostics available in health care system. In absence of this guidance, most of these diagnostics will sit with the innovators/developers and will never be used for the purpose they were intended to serve.
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Affiliation(s)
- Monica Sharma
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Raman R Gangakhedkar
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Sanjay Bhattacharya
- Department of Microbiology, Tata Medical Center, Kolkata, West Bengal, India
| | - Kamini Walia
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
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89
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Sun L, Chen Y, Duan Y, Ma F. Electrogenerated Chemiluminescence Biosensor Based on Functionalized Two-Dimensional Metal-Organic Frameworks for Bacterial Detection and Antimicrobial Susceptibility Assays. ACS APPLIED MATERIALS & INTERFACES 2021; 13:38923-38930. [PMID: 34369161 DOI: 10.1021/acsami.1c11949] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The emergence of antibiotic resistance has prompted the development of rapid antimicrobial susceptibility testing (AST) technologies to guide antibiotic prescription. A novel electrochemiluminescence (ECL) biosensor developed can quantitatively measure the binding between the lectin and lipopolysaccharide (LPS) on Gram-negative bacteria for bacterial determination and to characterize the antimicrobial activities of β-lactam and non-β-lactam antibiotics to normal and antibiotic-resistant bacteria. The biosensor utilizes ruthenium complex tagged concanavalin A (Ru-Con A) coated on NH2-MIL-53(Al) interface for LPS binding measurements. The decreased ECL signal obtained was directly proportional to increasing Escherichia coli (E. coli) BL21 concentrations. The sensitivity displayed logarithmic dependence in the range of (50-5.0) × 104 cells/mL, with a detection limit of 16 cells/mL. The minimum inhibitory concentration (MIC) values of antibiotics for normal E. coli BL21 were 0.02-0.2, 2-4, 0.002-0.02, and 0.2-1 mg/L for levofloxacin hydrochloride (LVX), tetracycline (TCY), imipenem (IPM), and cefpirome (CPO), respectively. The increased MIC values (8-16 and 4 mg/L for IMP and CPO, respectively) in New Delhi metallo-β-lactamase-1 expressing E. coli BL21 (NDM-1-E. coli BL21) indicated greater resistance to β-lactams in NDM-1-E. coli BL21 compared with normal E. coli BL21. Therefore, the changed ECL signal because of binding between LPS with the lectin has a relation with the type of antibiotic and bacterial strains, making the ECL biosensor promote clinical practicability and facilitate antibiotic stewardship.
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Affiliation(s)
- Lina Sun
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi 710127, People's Republic of China
| | - Yu Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi 710127, People's Republic of China
| | - Yuhong Duan
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi 710127, People's Republic of China
| | - Fen Ma
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an, Shaanxi 710127, People's Republic of China
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90
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Zhong J, Liang M, Ai Y. Submicron-precision particle characterization in microfluidic impedance cytometry with double differential electrodes. LAB ON A CHIP 2021; 21:2869-2880. [PMID: 34236057 DOI: 10.1039/d1lc00481f] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Submicron-precision particle characterization is crucial for counting, sizing and identifying a variety of biological particles, such as bacteria and apoptotic bodies. Microfluidic impedance cytometry has been attractive in current research for microparticle characterization due to its advantages of label-free detection, ease of miniaturization and affordability. However, conventional electrode configurations of three electrodes and floating electrodes have not yet demonstrated the capability of probing submicron particles or microparticles with a submicron size difference. In this study, we present a label-free high-throughput (∼800 particles per second) impedance-based microfluidic flow cytometry system integrated with a novel design of a double differential electrode configuration, enabling submicron particle detection (down to 0.4 μm) with a minimum size resolution of 200 nm. The signal-to-noise ratio has been boosted from 13.98 dB to 32.64 dB compared to a typical three-electrode configuration. With the proposed microfluidic impedance cytometry, we have shown results of sizing microparticles that accurately correlate with manufacturers' datasheets (R2 = 0.99938). It also shows that population ratios of differently sized beads in mixture samples are consistent with the results given by commercial fluorescence-based flow cytometry (within ∼1% difference). This work provides a label-free approach with submicron precision for sizing and counting microscale and submicron particles, and a new avenue of designing electrode configurations with a feature of suppressing the electrical noise for accomplishing a high signal-to-noise ratio in a wide range of frequencies. This novel double differential impedance sensing system paves a new pathway for real-time analysis and accurate particle screening in pathological and pharmacological research.
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Affiliation(s)
- Jianwei Zhong
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore.
| | - Minhui Liang
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore.
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore.
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91
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Evaluation of FASTinov® ultra-rapid flow cytometry antimicrobial susceptibility testing directly from positive blood cultures. J Clin Microbiol 2021; 59:e0054421. [PMID: 34346718 DOI: 10.1128/jcm.00544-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ultra-rapid antimicrobial susceptibility test FASTinov® flow cytometry kit was directly evaluated on positive blood cultures (BC) at two sites: i) FASTinov® in Porto (Portugal) using spiked BC with well-characterized bacteria and ii) Ramon y Cajal University hospital in Madrid (Spain) using patients positive BC. Two kits were evaluated, FASTgramneg (Enterobacterales, Pseudomonas, Acinetobacter) and FASTgrampos (Staphylococcus, Enterococcus). A dedicated software for cytometric data analysis and interpretative reporting, both using CLSI and EUCAST criteria, were used. The FASTgramneg kit also provides information about the presence of resistant mechanisms, including ESBLs and carbapenemases. After 1-h incubation at 37°C bacteria were analysed by CytoFLEX® cytometer (Beckman, CA). Disk diffusion was performed as reference susceptibility method. Overall, 447 positive BC were included, 100 from hospitalized patients. Categorical agreement for FASTgramneg panel was 96.8% for EUCAST and 96.4% for CLSI. For FASTgrampos panel it was 98.6% when using both criteria. Using EUCAST criteria the percentage of errors for FASTgramneg panel was 2.1% minor errors (mE), 1.3% major errors (ME) and 0.6% very major errors (VME). Concerning CLSI, 2.9% mE, 0.9% ME and 0.4% VME were found. VMEs were mainly observed with amoxicillin-clavulanate, cefotaxime, ceftazidime and gentamicin. FASTgrampos panel showed 0.3% mE, 1.4% ME and 0.4% VME using EUCAST criteria (VME regarded gentamicin and Staphylococcus) while 0.4% mE, 1.4% ME and no VME when using CLSI criteria. FASTinov® flow cytometry kits represent a rapid alternative for direct antimicrobial susceptibility testing from positive BC, showing time-to-results <2-h, which can be used to personalized antibiotics and stewardship practices.
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92
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Chan CW, Sun H, Wang Y, Zhao Z, O'Neill R, Siu SY, Chu X, Banaei N, Ren K. "Barcode" cell sensor microfluidic system: Rapid and sample-to-answer antimicrobial susceptibility testing applicable in resource-limited conditions. Biosens Bioelectron 2021; 192:113516. [PMID: 34330036 DOI: 10.1016/j.bios.2021.113516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 12/24/2022]
Abstract
Many rapid antimicrobial susceptibility testing (AST) methods have been proposed to contain clinical antimicrobial resistance (AMR) and preserve the effectiveness of remaining antimicrobials. However, far fewer methods have been proposed to test AMR in resource-limited conditions, such as for frequent safety screenings of water/food/public facilities, urgent surveys of massive samples during a pandemic, or AMR tests in low-income countries. Rapid AST methods realized thus far have a variety of drawbacks when used for such surveys, e.g., high cost and the requirement of expensive instruments such as microscopy. A more reasonable strategy would be to screen samples via onsite testing first, and then send any sample suspected to contain AMR bacteria for advanced testing. Accordingly, a cost-efficient AST is demanded, which can rapidly process a large number of samples without using expensive equipment. To this end, current work demonstrates a novel "barcode" cell sensor based on an adaptive linear filter array as a fully automatic and microscope-free method for counting very small volumes of cells (~1.00 × 104 cells without pre-incubation), wherein suspended cells concentrate into microbars with length proportional to the number of cells. We combined this sensor with an on-chip culture approach we had demonstrated for rapid and automated drug exposure and realized a low-cost and resource-independent platform for portable AST, from which results can be obtained simply through a cell phone. This method has a much shorter turnaround time (2-3 h) than that of standard methods (16-24 h). Thanks to its microscopy-free analysis, affordability, portability, high throughput, and user-friendliness, our "barcode" AST system has the potential to fulfill the various demands of AST when advanced facilities are not available, making it a promising new tool in the fight against AMR.
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Affiliation(s)
- Chiu-Wing Chan
- Department of Chemistry, Hong Kong Baptist University. Waterloo Road, Kowloon, Hong Kong, China
| | - Han Sun
- Department of Chemistry, Hong Kong Baptist University. Waterloo Road, Kowloon, Hong Kong, China
| | - Yisu Wang
- Department of Chemistry, Hong Kong Baptist University. Waterloo Road, Kowloon, Hong Kong, China
| | - Zhihao Zhao
- Department of Computer Science, Hong Kong Baptist University. Waterloo Road, Kowloon, Hong Kong, China
| | - Ryan O'Neill
- Department of Chemistry, Hong Kong Baptist University. Waterloo Road, Kowloon, Hong Kong, China; Department of Chemistry, Georgia State University, Atlanta, GA, United States
| | - Sin-Yung Siu
- Department of Chemistry, Hong Kong Baptist University. Waterloo Road, Kowloon, Hong Kong, China
| | - Xiaowen Chu
- Department of Computer Science, Hong Kong Baptist University. Waterloo Road, Kowloon, Hong Kong, China
| | - Niaz Banaei
- Department of Pathology Clinical, Stanford University School of Medicine, Stanford, CA, United States
| | - Kangning Ren
- Department of Chemistry, Hong Kong Baptist University. Waterloo Road, Kowloon, Hong Kong, China; HKBU Institute of Research and Continuing Education, Shenzhen, China; State Key Laboratory of Environmental and Biological Analysis, The Hong Kong Baptist University, Waterloo Road, Kowloon, Hong Kong, China.
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93
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van Belkum A, Almeida C, Bardiaux B, Barrass SV, Butcher SJ, Çaykara T, Chowdhury S, Datar R, Eastwood I, Goldman A, Goyal M, Happonen L, Izadi-Pruneyre N, Jacobsen T, Johnson PH, Kempf VAJ, Kiessling A, Bueno JL, Malik A, Malmström J, Meuskens I, Milner PA, Nilges M, Pamme N, Peyman SA, Rodrigues LR, Rodriguez-Mateos P, Sande MG, Silva CJ, Stasiak AC, Stehle T, Thibau A, Vaca DJ, Linke D. Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens. Diagnostics (Basel) 2021; 11:diagnostics11071259. [PMID: 34359341 PMCID: PMC8305138 DOI: 10.3390/diagnostics11071259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/18/2022] Open
Abstract
Infectious diseases are an existential health threat, potentiated by emerging and re-emerging viruses and increasing bacterial antibiotic resistance. Targeted treatment of infectious diseases requires precision diagnostics, especially in cases where broad-range therapeutics such as antibiotics fail. There is thus an increasing need for new approaches to develop sensitive and specific in vitro diagnostic (IVD) tests. Basic science and translational research are needed to identify key microbial molecules as diagnostic targets, to identify relevant host counterparts, and to use this knowledge in developing or improving IVD. In this regard, an overlooked feature is the capacity of pathogens to adhere specifically to host cells and tissues. The molecular entities relevant for pathogen–surface interaction are the so-called adhesins. Adhesins vary from protein compounds to (poly-)saccharides or lipid structures that interact with eukaryotic host cell matrix molecules and receptors. Such interactions co-define the specificity and sensitivity of a diagnostic test. Currently, adhesin-receptor binding is typically used in the pre-analytical phase of IVD tests, focusing on pathogen enrichment. Further exploration of adhesin–ligand interaction, supported by present high-throughput “omics” technologies, might stimulate a new generation of broadly applicable pathogen detection and characterization tools. This review describes recent results of novel structure-defining technologies allowing for detailed molecular analysis of adhesins, their receptors and complexes. Since the host ligands evolve slowly, the corresponding adhesin interaction is under selective pressure to maintain a constant receptor binding domain. IVD should exploit such conserved binding sites and, in particular, use the human ligand to enrich the pathogen. We provide an inventory of methods based on adhesion factors and pathogen attachment mechanisms, which can also be of relevance to currently emerging pathogens, including SARS-CoV-2, the causative agent of COVID-19.
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Affiliation(s)
- Alex van Belkum
- BioMérieux, Open Innovation & Partnerships, 38390 La Balme Les Grottes, France;
- Correspondence: (A.v.B.); (D.L.)
| | | | - Benjamin Bardiaux
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Sarah V. Barrass
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
| | - Sarah J. Butcher
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
| | - Tuğçe Çaykara
- Centre for Nanotechnology and Smart Materials, 4760-034 Vila Nova de Famalicão, Portugal; (T.Ç.); (C.J.S.)
| | - Sounak Chowdhury
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Rucha Datar
- BioMérieux, Microbiology R&D, 38390 La Balme Les Grottes, France;
| | | | - Adrian Goldman
- Department of Biological Sciences, University of Helsinki, 00014 Helsinki, Finland; (S.V.B.); (S.J.B.); (A.G.)
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Manisha Goyal
- BioMérieux, Open Innovation & Partnerships, 38390 La Balme Les Grottes, France;
| | - Lotta Happonen
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Theis Jacobsen
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Pirjo H. Johnson
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Volkhard A. J. Kempf
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Andreas Kiessling
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Juan Leva Bueno
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Anchal Malik
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Johan Malmström
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, 22242 Lund, Sweden; (S.C.); (L.H.); (J.M.)
| | - Ina Meuskens
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway;
| | - Paul A. Milner
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Michael Nilges
- Institut Pasteur, Structural Biology and Chemistry, 75724 Paris, France; (B.B.); (N.I.-P.); (T.J.); (M.N.)
| | - Nicole Pamme
- School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK; (N.P.); (P.R.-M.)
| | - Sally A. Peyman
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK; (P.H.J.); (A.K.); (J.L.B.); (A.M.); (P.A.M.); (S.A.P.)
| | - Ligia R. Rodrigues
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (L.R.R.); (M.G.S.)
| | - Pablo Rodriguez-Mateos
- School of Mathematics and Physical Sciences, University of Hull, Hull HU6 7RX, UK; (N.P.); (P.R.-M.)
| | - Maria G. Sande
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (L.R.R.); (M.G.S.)
| | - Carla Joana Silva
- Centre for Nanotechnology and Smart Materials, 4760-034 Vila Nova de Famalicão, Portugal; (T.Ç.); (C.J.S.)
| | - Aleksandra Cecylia Stasiak
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; (A.C.S.); (T.S.)
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany; (A.C.S.); (T.S.)
| | - Arno Thibau
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Diana J. Vaca
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, 60596 Frankfurt am Main, Germany; (V.A.J.K.); (A.T.); (D.J.V.)
| | - Dirk Linke
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway;
- Correspondence: (A.v.B.); (D.L.)
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94
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Bruce A, Adam KE, Buller H, Chan KW(R, Tait J. Creating an innovation ecosystem for rapid diagnostic tests for livestock to support sustainable antibiotic use. TECHNOLOGY ANALYSIS & STRATEGIC MANAGEMENT 2021. [DOI: 10.1080/09537325.2021.1950678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Ann Bruce
- Innogen Institute, Science Technology and Innovation Studies, School of Social and Political Science, University of Edinburgh, Edinburgh, UK
| | - Katherine E. Adam
- Innogen Institute, Science Technology and Innovation Studies, School of Social and Political Science, University of Edinburgh, Edinburgh, UK
| | - Henry Buller
- College of Life and Environmental Sciences, Department of Geography, University of Exeter, Exeter, UK
| | - Kin Wing (Ray) Chan
- College of Life and Environmental Sciences, Department of Geography, University of Exeter, Exeter, UK
| | - Joyce Tait
- Innogen Institute, Science Technology and Innovation Studies, School of Social and Political Science, University of Edinburgh, Edinburgh, UK
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95
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Michael CA, Gillings MR, Blaskovich MAT, Franks AE. The Antimicrobial Resistance Crisis: An Inadvertent, Unfortunate but Nevertheless Informative Experiment in Evolutionary Biology. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.692674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The global rise of antimicrobial resistance (AMR) phenotypes is an exemplar for rapid evolutionary response. Resistance arises as a consequence of humanity’s widespread and largely indiscriminate use of antimicrobial compounds. However, some features of this crisis remain perplexing. The remarkably widespread and rapid rise of diverse, novel and effective resistance phenotypes is in stark contrast to the apparent paucity of antimicrobial producers in the global microbiota. From the viewpoint of evolutionary theory, it should be possible to use selection coefficients to examine these phenomena. In this work we introduce an elaboration on the selection coefficient s termed selective efficiency, considering the genetic, metabolic, ecological and evolutionary impacts that accompany selective phenotypes. We then demonstrate the utility of the selective efficiency concept using AMR and antimicrobial production phenotypes as ‘worked examples’ of the concept. In accomplishing this objective, we also put forward cogent hypotheses to explain currently puzzling aspects of the AMR crisis. Finally, we extend the selective efficiency concept into a consideration of the ongoing management of the AMR crisis.
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96
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Rousseau AN, Faure N, Rol F, Sedaghat Z, Le Galudec J, Mallard F, Josso Q. Fast Antibiotic Susceptibility Testing via Raman Microspectrometry on Single Bacteria: An MRSA Case Study. ACS OMEGA 2021; 6:16273-16279. [PMID: 34235297 PMCID: PMC8246468 DOI: 10.1021/acsomega.1c00170] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/05/2021] [Indexed: 05/14/2023]
Abstract
Despite recent advances in molecular diagnostics, ultrafast determination of the antibiotic susceptibility phenotype of pathogenic microorganisms is still a major challenge of in vitro diagnostics (IVD) of infectious diseases. Raman microspectroscopy has been proposed as a means to achieve this goal. Previous studies have shown that susceptibility phenotyping could be done through Raman analysis of microbial cells, either in large clusters or down to the single-cell level in the case of Gram-negative rods. Gram-positive cocci such as Staphylococcus aureus pose several challenges due to their size and their different metabolic and chemical characteristics. Using a tailored automated single-cell Raman spectrometer and a previously proposed sample preparation protocol, we acquired and analyzed 9429 S. aureus single cells belonging to three cefoxitin-resistant strains and two susceptible strains during their incubation in the presence of various concentrations of cefoxitin. We observed an effect on S. aureus spectra that is weaker than what was detected on previous bacteria/drug combinations, with a higher cell-to-cell response variability and an important impact of incubation conditions on the phenotypic resistance of a given strain. Overall, the proposed protocol was able to correlate strains' phenotype with a specific modification of the spectra using majority votes. We, hence, confirm that our previous results on single-cell Raman antibiotic susceptibility testing can be extended to the S. aureus case and further clarify potential limitations and development requirements of this approach in the move toward industrial applications.
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Affiliation(s)
| | - Nicolas Faure
- bioMérieux,
R&D Microbiology, 5 rue des Berges, 38024 Grenoble, France
| | - Fabian Rol
- Bioaster, 40 avenue Tony Garnier, 69007 Lyon, France
| | | | - Joël Le Galudec
- bioMérieux,
R&D Microbiology, 5 rue des Berges, 38024 Grenoble, France
| | - Frédéric Mallard
- bioMérieux,
R&D Microbiology, 5 rue des Berges, 38024 Grenoble, France
| | - Quentin Josso
- bioMérieux,
R&D Microbiology, 376 Chemin de l’Orme, 69280 Marcy-l’Etoile, France
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97
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Jonasson E, Matuschek E, Kahlmeter G. The EUCAST rapid disc diffusion method for antimicrobial susceptibility testing directly from positive blood culture bottles. J Antimicrob Chemother 2021; 75:968-978. [PMID: 32016342 PMCID: PMC7069491 DOI: 10.1093/jac/dkz548] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/03/2019] [Accepted: 12/09/2019] [Indexed: 12/25/2022] Open
Abstract
Objectives With increasing antimicrobial resistance, rapid antimicrobial susceptibility testing (RAST) becomes important, especially in patients with bloodstream infections. EUCAST decided to develop a standardized rapid method, based on EUCAST disc diffusion, to offer susceptibility reports within 4–8 h of a positive blood culture (BC). Methods BC bottles were spiked with clinical isolates (n = 332) of the seven most relevant sepsis pathogens with a variety of resistance mechanisms. RAST was performed directly from the bottle and zones read after 4, 6 and 8 h. Several variables were investigated, including the effect of using different BC bottles and of a 0–18 h delay between a positive signal and the performance of RAST. Results For five species, most inhibition zones could be read after 4 h. The proportion of results that could be interpreted increased from 75% at 4 h to 84% after 8 h. Categorical agreement against the reference method was good, with error rates of false susceptibility of 0.2%, 0.2% and 0.2% at 4, 6 and 8 h and false resistance of 1.2%, 0.2% and 0.1% at 4, 6 and 8 h, respectively. Conclusions With the EUCAST RAST method, reliable AST results can be delivered within 4–8 h of positivity of BC bottles for seven important bloodstream infection pathogens. To reduce the occurrence of errors and to absorb the variability caused by using a non-standardized inoculum, material from different manufacturers and workflow-related delays, we have introduced an area in which interpretation is not permitted, the Area of Technical Uncertainty.
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Affiliation(s)
- Emma Jonasson
- Department of Clinical Microbiology, Central Hospital, Växjö, Sweden
| | | | - Gunnar Kahlmeter
- Department of Clinical Microbiology, Central Hospital, Växjö, Sweden.,EUCAST Development Laboratory, Växjö, Sweden
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98
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Lam CN, Mehta-Kolte MG, Martins-Sorenson N, Eckert B, Lin PH, Chu K, Moghaddasi A, Goldman D, Nguyen H, Chan R, Nukala L, Suko S, Hanson B, Yuan R, Cady KC. A Tail Fiber Engineering Platform for Improved Bacterial Transduction-Based Diagnostic Reagents. ACS Synth Biol 2021; 10:1292-1299. [PMID: 33983709 DOI: 10.1021/acssynbio.1c00036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bacterial transduction particles were critical to early advances in molecular biology and are currently experiencing a resurgence in interest within the diagnostic and therapeutic fields. The difficulty of developing a robust and specific transduction reagent capable of delivering a genetic payload to the diversity of strains constituting a given bacterial species or genus is a major impediment to their expanded utility as commercial products. While recent advances in engineering the reactivity of these reagents have made them more attractive for product development, considerable improvements are still needed. Here, we demonstrate a synthetic biology platform derived from bacteriophage P1 as a chassis to target transduction reagents against four clinically prevalent species within the Enterobacterales order. Bacteriophage P1 requires only a single receptor binding protein to enable attachment and injection into a target bacterium. By engineering and screening particles displaying a diverse array of chimeric receptor binding proteins, we generated a potential transduction reagent for a future rapid phenotypic carbapenem-resistant Enterobacterales diagnostic assay.
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Affiliation(s)
- Colin N. Lam
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | | | | | - Barbara Eckert
- Roche Molecular Systems, Pleasanton, California 94588, United States
| | - Patrick H. Lin
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Kristina Chu
- Roche Molecular Systems, Pleasanton, California 94588, United States
| | - Arrash Moghaddasi
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Dylan Goldman
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Hai Nguyen
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Ryan Chan
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Laxmi Nukala
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Shawn Suko
- Roche Molecular Systems, Pleasanton, California 94588, United States
| | - Brett Hanson
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Richard Yuan
- Roche Molecular Systems, Santa Clara, California 95050, United States
| | - Kyle C. Cady
- Roche Molecular Systems, Santa Clara, California 95050, United States
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99
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Abstract
The advent of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in clinical microbiology has dramatically improved the accuracy and speed of diagnostics. However, this progress has mainly been limited to the identification of microorganisms, whereas the practical improvement of antimicrobial susceptibility testing (AST) still lags behind. MALDI-TOF MS-based approaches include the detection of selected resistance mechanisms and the universal phenotypic AST. This minireview focuses on the discussion of those MALDI-TOF MS methods that allow universal growth-based phenotypic AST. The method of minimal profile change concentrations (MPCC) is based on detecting proteome modification in presence of an antimicrobial. Using stable-isotope labeling, characteristic mass shifts in the presence of an antimicrobial indicate the incorporation of the isotopic labels, and, thus, the viability and resistance of the microorganism. For MALDI Biotyper antibiotic susceptibility test rapid assay (MBT-ASTRA), microorganisms are incubated with or without an antimicrobial, followed by cell lysis, protein extraction, and transfer of the cell lysate onto a MALDI target plate. Using the internal standard, peak intensities are correlated to the amount of microbial proteins, and the relative microbial growth is calculated. Most recent development in the field is the direct-on-target microdroplet growth assay (DOT-MGA). Here, incubation of microorganisms with antimicrobials takes place directly on spots of a MALDI target in form of microdroplets. After incubation, nutrient medium is removed by dabbing with absorptive material. Resistant microorganisms grow despite the presence of antimicrobial, and their amplified biomass is detected by MALDI-TOF MS. Finally, an outlook is provided for further assay improvements.
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100
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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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