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Wang Y, Jiang S, Fu Q, Wang X, Zhang Z, Lyu X, Yao X, Qu Z, Zhao Y, Huang JA, Li Y. Unmasking Bacterial Identities: Exploiting Silver Nanoparticle 'Masks' for Enhanced Raman Scattering in the Rapid Discrimination of Diverse Bacterial Species and Antibiotic-Resistant Strains. Anal Chem 2024; 96:8566-8575. [PMID: 38748451 DOI: 10.1021/acs.analchem.4c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Unraveling bacterial identity through Raman scattering techniques has been persistently challenging due to homogeneously amplified Raman signals across a wide variety of bacterial molecules, predominantly protein- or nucleic acid-mediated. In this study, we present an approach involving the use of silver nanoparticles to completely and uniformly "mask" adsorption on the surface of bacterial molecules through sodium borohydride and sodium chloride. This approach enables the acquisition of enhanced surface-enhanced Raman scattering (SERS) signals from all components on the bacterial surface, facilitating rapid, specific, and label-free bacterial identification. For the first time, we have characterized the identity of a bacterium, including its DNA, metabolites, and cell walls, enabling the accurate differentiation of various bacterial strains, even within the same species. In addition, we embarked on an exploration of the origin and variability patterns of the main characteristic peaks of Gram-positive and Gram-negative bacteria. Significantly, the SERS peak ratio was found to determine the inflection point of accelerated bacterial death upon treatment with antimicrobials. We further applied this platform to identify 15 unique clinical antibiotic-resistant bacterial strains, including five Escherichia coli strains in human urine, a first for Raman technology. This work has profound implications for prompt and accurate identification of bacteria, particularly antibiotic-resistant strains, thereby significantly enhancing clinical diagnostics and antimicrobial treatment strategies.
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Affiliation(s)
- Yunpeng Wang
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD); Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, No. 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province 150081, China
| | - Shen Jiang
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD); Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, No. 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province 150081, China
| | - Qiang Fu
- Department of Chinese Formulae, Heilongjiang University of Chinese Medicine, No. 24 Heping Road, Xiangfang District, Harbin City, Heilongjiang Province 150081, China
| | - Xiaotong Wang
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD); Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, No. 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province 150081, China
| | - Zhe Zhang
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD); Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, No. 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province 150081, China
| | - Xiaoming Lyu
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD); Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, No. 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province 150081, China
| | - Xinyu Yao
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD); Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, No. 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province 150081, China
| | - Zhangyi Qu
- School of Public Health, Harbin Medical University, No. 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province 150081, China
| | - Yingqi Zhao
- Faculty of Medicine, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu 90014, Finland
| | - Jian-An Huang
- Faculty of Medicine, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu 90014, Finland
| | - Yang Li
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD); Research Center for Innovative Technology of Pharmaceutical Analysis, College of Pharmacy, Harbin Medical University, No. 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province 150081, China
- Research Unit of Health Sciences and Technology (HST), Faculty of Medicine University of Oulu, Oulu 90014, Finland
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Rangel K, De-Simone SG. Treatment and Management of Acinetobacter Pneumonia: Lessons Learned from Recent World Event. Infect Drug Resist 2024; 17:507-529. [PMID: 38348231 PMCID: PMC10860873 DOI: 10.2147/idr.s431525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 01/23/2024] [Indexed: 02/15/2024] Open
Abstract
Acinetobacter pneumonia is a significant healthcare-associated infection that poses a considerable challenge to clinicians due to its multidrug-resistant nature. Recent world events, such as the COVID-19 pandemic, have highlighted the need for effective treatment and management strategies for Acinetobacter pneumonia. In this review, we discuss lessons learned from recent world events, particularly the COVID-19 pandemic, in the context of the treatment and management of Acinetobacter pneumonia. We performed an extensive literature review to uncover studies and information pertinent to the topic. The COVID-19 pandemic underscored the importance of infection control measures in healthcare settings, including proper hand hygiene, isolation protocols, and personal protective equipment use, to prevent the spread of multidrug-resistant pathogens like Acinetobacter. Additionally, the pandemic highlighted the crucial role of antimicrobial stewardship programs in optimizing antibiotic use and curbing the emergence of resistance. Advances in diagnostic techniques, such as rapid molecular testing, have also proven valuable in identifying Acinetobacter infections promptly. Furthermore, due to the limited availability of antibiotics for treating infections caused A. baumannii, alternative strategies are needed like the use of antimicrobial peptides, bacteriophages and their enzymes, nanoparticles, photodynamic and chelate therapy. Recent world events, particularly the COVID-19 pandemic, have provided valuable insights into the treatment and management of Acinetobacter pneumonia. These lessons emphasize the significance of infection control, antimicrobial stewardship, and early diagnostics in combating this challenging infection.
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Affiliation(s)
- Karyne Rangel
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, 21040-900, Brazil
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, 21040-900, Brazil
| | - Salvatore Giovanni De-Simone
- Center for Technological Development in Health (CDTS)/National Institute of Science and Technology for Innovation in Neglected Population Diseases (INCT-IDPN), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, 21040-900, Brazil
- Epidemiology and Molecular Systematics Laboratory (LEMS), Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, 21040-900, Brazil
- Program of Post-Graduation on Science and Biotechnology, Department of Molecular and Cellular Biology, Biology Institute, Federal Fluminense University, Niterói, RJ, 22040-036, Brazil
- Program of Post-Graduation on Parasitic Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, 21040-900, Brazil
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3
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Liu Y, Xu Y, Xu X, Chen X, Chen H, Zhang J, Ma J, Zhang W, Zhang R, Chen J. Metagenomic identification of pathogens and antimicrobial-resistant genes in bacterial positive blood cultures by nanopore sequencing. Front Cell Infect Microbiol 2023; 13:1283094. [PMID: 38192400 PMCID: PMC10773726 DOI: 10.3389/fcimb.2023.1283094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/30/2023] [Indexed: 01/10/2024] Open
Abstract
Nanopore sequencing workflows have attracted increasing attention owing to their fast, real-time, and convenient portability. Positive blood culture samples were collected from patients with bacterial bloodstream infection and tested by nanopore sequencing. This study compared the sequencing results for pathogen taxonomic profiling and antimicrobial resistance genes to those of species identification and phenotypic drug susceptibility using traditional microbiology testing. A total of 37 bacterial positive blood culture results of strain genotyping by nanopore sequencing were consistent with those of mass spectrometry. Among them, one mixed infection of bacteria and fungi was identified using nanopore sequencing and confirmatory quantitative polymerase chain reaction. The amount of sequencing data was 21.89 ± 8.46 MB for species identification, and 1.0 MB microbial strain data enabled accurate determination. Data volumes greater than or equal to 94.6 MB nearly covered all the antimicrobial resistance genes of the bacteria in our study. In addition, the results of the antimicrobial resistance genes were compared with those of phenotypic drug susceptibility testing for Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. Therefore, the nanopore sequencing platform for rapid identification of causing pathogens and relevant antimicrobial resistance genes complementary to conventional blood culture outcomes may optimize antimicrobial stewardship management for patients with bacterial bloodstream infection.
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Affiliation(s)
- Yahui Liu
- Department of Laboratory Medicine, Shanghai Xuhui District Central Hospital & Fudan University Affiliated Xuhui Hospital, Shanghai, China
- Department of Laboratory Medicine, Shanghai Post and Telecommunication Hospital, Shanghai, China
| | - Yumei Xu
- Department of Laboratory Medicine, Shanghai Xuhui District Central Hospital & Fudan University Affiliated Xuhui Hospital, Shanghai, China
| | - Xinyu Xu
- Department of Laboratory Medicine, Shanghai Post and Telecommunication Hospital, Shanghai, China
| | - Xianghui Chen
- Shanghai Diabetes Institute, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongli Chen
- Shanghai Diabetes Institute, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingjing Zhang
- Precision Medicine Center, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiayu Ma
- Precision Medicine Center, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenrui Zhang
- Precision Medicine Center, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rong Zhang
- Shanghai Diabetes Institute, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Chen
- Department of Laboratory Medicine, Shanghai Post and Telecommunication Hospital, Shanghai, China
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4
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Lewinski MA, Alby K, Babady NE, Butler-Wu SM, Bard JD, Greninger AL, Hanson K, Naccache SN, Newton D, Temple-Smolkin RL, Nolte F. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. J Mol Diagn 2023; 25:857-875. [PMID: 37757952 DOI: 10.1016/j.jmoldx.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The use of clinical molecular diagnostic methods for detecting microbial pathogens continues to expand and, in some cases, supplant conventional identification methods in various scenarios. Analytical and clinical benefits of multiplex molecular panels for the detection of respiratory pathogens have been demonstrated in various studies. The use of these panels in managing different patient populations has been incorporated into clinical guidance documents. The Association for Molecular Pathology's Infectious Diseases Multiplex Working Group conducted a review of the current benefits and challenges to using multiplex PCR for the detection of pathogens from gastrointestinal tract, central nervous system, lower respiratory tract, and joint specimens. The Working Group also discusses future directions and novel approaches to detection of pathogens in alternate specimen types, and outlines challenges associated with implementation of these multiplex PCR panels.
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Affiliation(s)
- Michael A Lewinski
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Roche Molecular Systems, San Clemente, California.
| | - Kevin Alby
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - N Esther Babady
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Clinical Microbiology Service, Departments of Laboratory Medicine and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan M Butler-Wu
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Clinical Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Jennifer Dien Bard
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alexander L Greninger
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Kimberly Hanson
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; University of Utah School of Medicine and ARUP Laboratories, Salt Lake City, Utah
| | - Samia N Naccache
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Microbiology, LabCorp Seattle, Seattle, Washington
| | - Duane Newton
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Bio-Rad Laboratories, Irvine, California
| | | | - Frederick Nolte
- Infectious Diseases Multiplex Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
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Abu-Aqil G, Lapidot I, Salman A, Huleihel M. Quick Detection of Proteus and Pseudomonas in Patients' Urine and Assessing Their Antibiotic Susceptibility Using Infrared Spectroscopy and Machine Learning. SENSORS (BASEL, SWITZERLAND) 2023; 23:8132. [PMID: 37836961 PMCID: PMC10575053 DOI: 10.3390/s23198132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
Bacterial resistance to antibiotics is a primary global healthcare concern as it hampers the effectiveness of commonly used antibiotics used to treat infectious diseases. The development of bacterial resistance continues to escalate over time. Rapid identification of the infecting bacterium and determination of its antibiotic susceptibility are crucial for optimal treatment and can save lives in many cases. Classical methods for determining bacterial susceptibility take at least 48 h, leading physicians to resort to empirical antibiotic treatment based on their experience. This random and excessive use of antibiotics is one of the most significant drivers of the development of multidrug-resistant (MDR) bacteria, posing a severe threat to global healthcare. To address these challenges, considerable efforts are underway to reduce the testing time of taxonomic classification of the infecting bacterium at the species level and its antibiotic susceptibility determination. Infrared spectroscopy is considered a rapid and reliable method for detecting minor molecular changes in cells. Thus, the main goal of this study was the use of infrared spectroscopy to shorten the identification and the susceptibility testing time of Proteus mirabilis and Pseudomonas aeruginosa from 48 h to approximately 40 min, directly from patients' urine samples. It was possible to identify the Proteus mirabilis and Pseudomonas aeruginosa species with 99% accuracy and, simultaneously, to determine their susceptibility to different antibiotics with an accuracy exceeding 80%.
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Affiliation(s)
- George Abu-Aqil
- Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Itshak Lapidot
- Department of Electrical Engineering, ACLP-Afeka Center for Language Processing, Afeka Tel-Aviv Academic College of Engineering, Tel-Aviv 69107, Israel;
- Laboratoire Informatique d’Avignon (LIA), Avignon Université, 339 Chemin des Meinajaries, 84000 Avignon, France
| | - Ahmad Salman
- Department of Physics, SCE-Shamoon College of Engineering, Beer-Sheva 84100, Israel
| | - Mahmoud Huleihel
- Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Song Y, Park N, Jo DA, Kim J, Yong D, Song J, Park YM, Lee SJ, Kim YT, Im SG, Choi BG, Kang T, Lee KG. Polyaniline-based 3D network structure promotes entrapment and detection of drug-resistant bacteria. NANO CONVERGENCE 2023; 10:25. [PMID: 37243716 PMCID: PMC10224663 DOI: 10.1186/s40580-023-00370-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/07/2023] [Indexed: 05/29/2023]
Abstract
Sensitive and accurate capture, enrichment, and identification of drug-resistant bacteria on human skin are important for early-stage diagnosis and treatment of patients. Herein, we constructed a three-dimensional hierarchically structured polyaniline nanoweb (3D HPN) to capture, enrich, and detect drug-resistant bacteria on-site by rubbing infected skins. These unique hierarchical nanostructures enhance bacteria capture efficiency and help severely deform the surface of the bacteria entrapped on them. Therefore, 3D HPN significantly contributes to the effective and reliable recovery of drug-resistant bacteria from the infected skin and the prevention of potential secondary infection. The recovered bacteria were successfully identified by subsequent real-time polymerase chain reaction (PCR) analysis after the lysis process. The molecular analysis results based on a real-time PCR exhibit excellent sensitivity to detecting target bacteria of concentrations ranging from 102 to 107 CFU/mL without any fluorescent signal interruption. To confirm the field applicability of 3D HPN, it was tested with a drug-resistant model consisting of micropig skin similar to human skin and Klebsiella pneumoniae carbapenemase-producing carbapenem-resistant Enterobacteriaceae (KPC-CRE). The results show that the detection sensitivity of this assay is 102 CFU/mL. Therefore, 3D HPN can be extended to on-site pathogen detection systems, along with rapid molecular diagnostics through a simple method, to recover KPC-CRE from the skin.
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Affiliation(s)
- Younseong Song
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Nahyun Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Da Ae Jo
- Center for Nano Bio Development, National Nanofab Center (NNFC), Daejeon, 34141, Republic of Korea
| | - Jueun Kim
- Center for Nano Bio Development, National Nanofab Center (NNFC), Daejeon, 34141, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jayeon Song
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Yoo Min Park
- Center for Nano Bio Development, National Nanofab Center (NNFC), Daejeon, 34141, Republic of Korea
| | - Seok Jae Lee
- Center for Nano Bio Development, National Nanofab Center (NNFC), Daejeon, 34141, Republic of Korea
| | - Yong Tae Kim
- Department of Chemical Engineering & Biotechnology, Tech University of Korea, Siheung-Si, 15073, Republic of Korea
| | - Sung Gap Im
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Bong Gill Choi
- Department of Chemical Engineering, Kangwon National University, Samcheok, 25913, Republic of Korea.
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University (SKKU), Suwon-Si, 16419, Republic of Korea.
| | - Kyoung G Lee
- Center for Nano Bio Development, National Nanofab Center (NNFC), Daejeon, 34141, Republic of Korea.
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Marutescu LG. Current and Future Flow Cytometry Applications Contributing to Antimicrobial Resistance Control. Microorganisms 2023; 11:1300. [PMID: 37317273 DOI: 10.3390/microorganisms11051300] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
Antimicrobial resistance is a global threat to human health and welfare, food safety, and environmental health. The rapid detection and quantification of antimicrobial resistance are important for both infectious disease control and public health threat assessment. Technologies such as flow cytometry can provide clinicians with the early information, they need for appropriate antibiotic treatment. At the same time, cytometry platforms facilitate the measurement of antibiotic-resistant bacteria in environments impacted by human activities, enabling assessment of their impact on watersheds and soils. This review focuses on the latest applications of flow cytometry for the detection of pathogens and antibiotic-resistant bacteria in both clinical and environmental samples. Novel antimicrobial susceptibility testing frameworks embedding flow cytometry assays can contribute to the implementation of global antimicrobial resistance surveillance systems that are needed for science-based decisions and actions.
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Affiliation(s)
- Luminita Gabriela Marutescu
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 91-95 Spl. Independentei, 050095 Bucharest, Romania
- Research Institute of the University of Bucharest, 050095 Bucharest, Romania
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Avershina E, Khezri A, Ahmad R. Clinical Diagnostics of Bacterial Infections and Their Resistance to Antibiotics-Current State and Whole Genome Sequencing Implementation Perspectives. Antibiotics (Basel) 2023; 12:antibiotics12040781. [PMID: 37107143 PMCID: PMC10135054 DOI: 10.3390/antibiotics12040781] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/19/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Antimicrobial resistance (AMR), defined as the ability of microorganisms to withstand antimicrobial treatment, is responsible for millions of deaths annually. The rapid spread of AMR across continents warrants systematic changes in healthcare routines and protocols. One of the fundamental issues with AMR spread is the lack of rapid diagnostic tools for pathogen identification and AMR detection. Resistance profile identification often depends on pathogen culturing and thus may last up to several days. This contributes to the misuse of antibiotics for viral infection, the use of inappropriate antibiotics, the overuse of broad-spectrum antibiotics, or delayed infection treatment. Current DNA sequencing technologies offer the potential to develop rapid infection and AMR diagnostic tools that can provide information in a few hours rather than days. However, these techniques commonly require advanced bioinformatics knowledge and, at present, are not suited for routine lab use. In this review, we give an overview of the AMR burden on healthcare, describe current pathogen identification and AMR screening methods, and provide perspectives on how DNA sequencing may be used for rapid diagnostics. Additionally, we discuss the common steps used for DNA data analysis, currently available pipelines, and tools for analysis. Direct, culture-independent sequencing has the potential to complement current culture-based methods in routine clinical settings. However, there is a need for a minimum set of standards in terms of evaluating the results generated. Additionally, we discuss the use of machine learning algorithms regarding pathogen phenotype detection (resistance/susceptibility to an antibiotic).
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Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata, 222317 Hamar, Norway
- Institute of Clinical Medicine, Faculty of Health Science, UiT The Arctic University of Norway, Hansine Hansens veg, 189019 Tromsø, Norway
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9
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Ali J, Joshi M, Ahmadi A, Strætkvern KO, Ahmad R. Increased growth temperature and vitamin B12 supplementation reduces the lag time for rapid pathogen identification in BHI agar and blood cultures. F1000Res 2023; 12:131. [PMID: 37122874 PMCID: PMC10133824 DOI: 10.12688/f1000research.129668.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
Background: Rapid diagnostics of pathogens is essential to prescribe appropriate antibiotic therapy. The current methods for pathogen detection require the bacteria to grow in a culture medium, which is time-consuming. This increases the mortality rate and global burden of antimicrobial resistance. Culture-free detection methods are still under development and are not common in the clinical routine. Therefore, decreasing the culture time for accurately detecting infection and resistance is vital for diagnosis. Methods: This study investigated easy-to-implement factors (in a minimal laboratory set-up), including inoculum size, incubation temperature, and additional supplementation (e.g., vitamin B12 and trace metals), that can significantly reduce the bacterial lag time (tlag). These factors were arranged in simple two-level factorial designs using Gram-positive cocci (Staphylococcus aureus), Gram-positive bacilli (Bacillus subtilis), and Gram-negative bacilli (Escherichia coli and Pseudomonas aeruginosa) bacteria, including clinical isolates with known antimicrobial resistance profiles. Blood samples spiked with a clinical isolate of E. coli CCUG 17620 (Culture Collection University of Gothenburg) were also tested to see the effect of elevated incubation temperature on bacterial growth in blood cultures. Results: We observed that increased incubation temperature (42°C) along with vitamin B12 supplementation significantly reduced the tlag (10 – 115 minutes or 4% - 49%) in pure clinical isolates and blood samples spiked with E. coli CCUG17620. In the case of the blood sample, PCR results also detected bacterial DNA after only 3h of incubation and at three times the CFU/mL. Conclusion: Enrichment of bacterial culture media with growth supplements such as vitamin B12 and increased incubation temperature can be a cheap and rapid method for the early detection of pathogens. This proof-of-concept study is restricted to a few bacterial strains and growth conditions. In the future, the effect of other growth conditions and difficult-to-culture bacteria should be explored to shorten the lag phase.
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Affiliation(s)
- Jawad Ali
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Mukund Joshi
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Asal Ahmadi
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Knut Olav Strætkvern
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
- Institute of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
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10
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Zhang X, Hou X, Ma L, Shi Y, Zhang D, Qu K. Analytical methods for assessing antimicrobial activity of nanomaterials in complex media: advances, challenges, and perspectives. J Nanobiotechnology 2023; 21:97. [PMID: 36941596 PMCID: PMC10026445 DOI: 10.1186/s12951-023-01851-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/07/2023] [Indexed: 03/23/2023] Open
Abstract
Assessing the antimicrobial activity of engineered nanomaterials (ENMs), especially in realistic scenarios, is of great significance for both basic research and applications. Multiple analytical methods are available for analysis via off-line or on-line measurements. Real-world samples are often complex with inorganic and organic components, which complicates the measurements of microbial viability and/or metabolic activity. This article highlights the recent advances achieved in analytical methods including typical applications and specifics regarding their accuracy, cost, efficiency, and user-friendliness. Methodological drawbacks, technique gaps, and future perspectives are also discussed. This review aims to help researchers select suitable methods for gaining insight into antimicrobial activities of targeted ENMs in artificial and natural complex matrices.
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Affiliation(s)
- Xuzhi Zhang
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiangyi Hou
- School of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, 201306, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Liangyu Ma
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Yaqi Shi
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Dahai Zhang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China.
| | - Keming Qu
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
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11
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Kalpana S, Lin WY, Wang YC, Fu Y, Lakshmi A, Wang HY. Antibiotic Resistance Diagnosis in ESKAPE Pathogens-A Review on Proteomic Perspective. Diagnostics (Basel) 2023; 13:1014. [PMID: 36980322 PMCID: PMC10047325 DOI: 10.3390/diagnostics13061014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Antibiotic resistance has emerged as an imminent pandemic. Rapid diagnostic assays distinguish bacterial infections from other diseases and aid antimicrobial stewardship, therapy optimization, and epidemiological surveillance. Traditional methods typically have longer turn-around times for definitive results. On the other hand, proteomic studies have progressed constantly and improved both in qualitative and quantitative analysis. With a wide range of data sets made available in the public domain, the ability to interpret the data has considerably reduced the error rates. This review gives an insight on state-of-the-art proteomic techniques in diagnosing antibiotic resistance in ESKAPE pathogens with a future outlook for evading the "imminent pandemic".
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Affiliation(s)
- Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
| | | | - Yu-Chiang Wang
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Yiwen Fu
- Department of Medicine, Kaiser Permanente Santa Clara Medical Center, Santa Clara, CA 95051, USA
| | - Amrutha Lakshmi
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, India
| | - Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
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12
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Ali J, Joshi M, Ahmadi A, Strætkvern KO, Ahmad R. Increased growth temperature and vitamin B12 supplementation reduces the lag time for rapid pathogen identification in BHI agar and blood cultures. F1000Res 2023; 12:131. [PMID: 37122874 PMCID: PMC10133824 DOI: 10.12688/f1000research.129668.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Background: The rapid diagnostics of pathogens is essential to prescribe appropriate and early antibiotic therapy. The current methods for pathogen detection require the bacteria to grow in a culture medium, which is time-consuming. This increases the mortality rate and the global burden of antimicrobial resistance. Culture-free detection methods are still under development and are not used in the clinical routine. Therefore decreasing the culture time for accurate detection of infection and resistance is vital for diagnosis. Methods: In this study, we wanted to investigate easy-to-implement factors (in a minimal laboratory set-up), including inoculum size, incubation temperature, and additional supplementation (e.g., vitamin B12 and trace metals), that can significantly reduce the lag time (tlag). These factors were arranged in simple two-level factorial designs using Gram-positive (Escherichia coli and Pseudomonas aeruginosa) and Gram-negative (Staphylococcus aureus and Bacillus subtilis) bacteria, including clinical isolates with known antimicrobial resistance profiles. Blood samples spiked with a clinical isolate of E. coli CCUG17620 were also tested to see the effect of elevated incubation temperature on bacterial growth in blood cultures. Results: We observed that increased incubation temperature (42°C) along with vitamin B12 supplementation significantly reduced the tlag (10 – 115 minutes or 4% - 49%) in pure clinical isolates and blood samples spiked with E. coli CCUG17620. In the case of the blood sample, PCR results also detected bacterial DNA after only 3h of incubation and at three times the CFU/mL. Conclusions: Enrichment of bacterial culture media with growth supplements such as vitamin B12 and increased incubation temperature can be a cheap and rapid method for the early detection of pathogens. This is a proof-of-concept study restricted to a few bacterial strains and growth conditions. In the future, the effect of other growth conditions and difficult-to-culture bacteria should be explored to shorten the lag phase.
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Affiliation(s)
- Jawad Ali
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Mukund Joshi
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Asal Ahmadi
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Knut Olav Strætkvern
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
- Institute of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
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13
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Blom K, Jørstad ØK, Faber RT, Stene-Johansen I, Holberg-Petersen M, Hermansen NO, Bragadóttir R. Primary vitrectomy or intravitreal antibiotics followed by early vitrectomy for acute endophthalmitis: A prospective observational study. Acta Ophthalmol 2023; 101:100-108. [PMID: 35751448 PMCID: PMC10084037 DOI: 10.1111/aos.15207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/30/2022] [Accepted: 06/05/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND/AIMS To compare outcomes of acute endophthalmitis (EO) managed with either primary vitrectomy (PV) or primary intravitreal antibiotics (vancomycin and ceftazidime) followed by early vitrectomy (PIAEV) combined with polymerase chain reaction (PCR)-based diagnostics. METHODS This was a prospective, comparative observational study of acute EO cases admitted to a regional vitreoretinal service over 18 months. Depending on whether immediate vitrectomy (within 6 h) was achievable, the EO cases were treated with either (1) PV or (2) PIAEV. Microbiology samples were collected either (A) before or (B) after administration of intravitreal antibiotics. The samples were analysed with broad-range 16S PCR and culture. RESULTS The study included 41 EO cases. There were 19 post-injection EO, 18 post-cataract EO, three post-vitrectomy EO, and one blebitis-related EO. Fifteen of 19 PV cases and 15 of 21 PIAEV had a clinically meaningful improvement in best-corrected visual acuity (BCVA) of at least 15 letters at 3 months (p = 0.58). One patient was lost to follow-up. Twenty-three cases were culture- and PCR-positive, and seven additional cases were culture-negative but PCR-positive (p = 0.02). PCR increased the diagnostic yield for samples collected both before and after administration of intravitreal antibiotics. CONCLUSION Primary vitrectomy or PIAEV allowed for vitrectomy for all cases of acute EO in a large region. Most eyes in both groups achieved a clinically meaningful improvement in BCVA. By combining culture with PCR in connection with the vitrectomy procedure, intravitreal antibiotics could be injected before microbiological sampling, thereby improving the door-to-treatment time without sacrificing microbial identification.
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Affiliation(s)
- Kathrine Blom
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Øystein Kalsnes Jørstad
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | | | | | | | - Ragnheiður Bragadóttir
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway.,Faculty of Medicine, University of Oslo, Oslo, Norway
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14
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Ahmad A, Hettiarachchi R, Khezri A, Singh Ahluwalia B, Wadduwage DN, Ahmad R. Highly sensitive quantitative phase microscopy and deep learning aided with whole genome sequencing for rapid detection of infection and antimicrobial resistance. Front Microbiol 2023; 14:1154620. [PMID: 37125187 PMCID: PMC10130531 DOI: 10.3389/fmicb.2023.1154620] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/16/2023] [Indexed: 05/02/2023] Open
Abstract
Current state-of-the-art infection and antimicrobial resistance (AMR) diagnostics are based on culture-based methods with a detection time of 48-96 h. Therefore, it is essential to develop novel methods that can do real-time diagnoses. Here, we demonstrate that the complimentary use of label-free optical assay with whole-genome sequencing (WGS) can enable rapid diagnosis of infection and AMR. Our assay is based on microscopy methods exploiting label-free, highly sensitive quantitative phase microscopy (QPM) followed by deep convolutional neural networks-based classification. The workflow was benchmarked on 21 clinical isolates from four WHO priority pathogens that were antibiotic susceptibility tested, and their AMR profile was determined by WGS. The proposed optical assay was in good agreement with the WGS characterization. Accurate classification based on the gram staining (100% recall for gram-negative and 83.4% for gram-positive), species (98.6%), and resistant/susceptible type (96.4%), as well as at the individual strain level (100% sensitivity in predicting 19 out of the 21 strains, with an overall accuracy of 95.45%). The results from this initial proof-of-concept study demonstrate the potential of the QPM assay as a rapid and first-stage tool for species, strain-level classification, and the presence or absence of AMR, which WGS can follow up for confirmation. Overall, a combined workflow with QPM and WGS complemented with deep learning data analyses could, in the future, be transformative for detecting and identifying pathogens and characterization of the AMR profile and antibiotic susceptibility.
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Affiliation(s)
- Azeem Ahmad
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ramith Hettiarachchi
- Department of Electronic and Telecommunication Engineering, University of Moratuwa, Moratuwa, Sri Lanka
- Center for Advanced Imaging, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, United States
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Balpreet Singh Ahluwalia
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
- Department of Clinical Science, Intervention and Technology, Karolinska Insitute, Stockholm, Sweden
| | - Dushan N. Wadduwage
- Center for Advanced Imaging, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, United States
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
- Institute of Clinical Medicine, Faculty of Health Sciences, UiT—The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Rafi Ahmad,
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15
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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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16
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Avershina E, Frye SA, Ali J, Taxt AM, Ahmad R. Ultrafast and Cost-Effective Pathogen Identification and Resistance Gene Detection in a Clinical Setting Using Nanopore Flongle Sequencing. Front Microbiol 2022; 13:822402. [PMID: 35369431 PMCID: PMC8970966 DOI: 10.3389/fmicb.2022.822402] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
Rapid bacterial identification and antimicrobial resistance gene (ARG) detection are crucial for fast optimization of antibiotic treatment, especially for septic patients where each hour of delayed antibiotic prescription might have lethal consequences. This work investigates whether the Oxford Nanopore Technology’s (ONT) Flongle sequencing platform is suitable for real-time sequencing directly from blood cultures to identify bacteria and detect resistance-encoding genes. For the analysis, we used pure bacterial cultures of four clinical isolates of Escherichia coli and Klebsiella pneumoniae and two blood samples spiked with either E. coli or K. pneumoniae that had been cultured overnight. We sequenced both the whole genome and plasmids isolated from these bacteria using two different sequencing kits. Generally, Flongle data allow rapid bacterial ID and resistome detection based on the first 1,000–3,000 generated sequences (10 min to 3 h from the sequencing start), albeit ARG variant identification did not always correspond to ONT MinION and Illumina sequencing-based data. Flongle data are sufficient for 99.9% genome coverage within at most 20,000 (clinical isolates) or 50,000 (positive blood cultures) sequences generated. The SQK-LSK110 Ligation kit resulted in higher genome coverage and more accurate bacterial identification than the SQK-RBK004 Rapid Barcode kit.
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Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Stephan A Frye
- Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jawad Ali
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Arne M Taxt
- Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway.,Faculty of Health Sciences, Institute of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
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17
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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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18
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Davidson SL, Niepa THR. Micro-Technologies for Assessing Microbial Dynamics in Controlled Environments. Front Microbiol 2022; 12:745835. [PMID: 35154021 PMCID: PMC8831547 DOI: 10.3389/fmicb.2021.745835] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
With recent advances in microfabrication technologies, the miniaturization of traditional culturing techniques has provided ideal methods for interrogating microbial communities in a confined and finely controlled environment. Micro-technologies offer high-throughput screening and analysis, reduced experimental time and resources, and have low footprint. More importantly, they provide access to culturing microbes in situ in their natural environments and similarly, offer optical access to real-time dynamics under a microscope. Utilizing micro-technologies for the discovery, isolation and cultivation of "unculturable" species will propel many fields forward; drug discovery, point-of-care diagnostics, and fundamental studies in microbial community behaviors rely on the exploration of novel metabolic pathways. However, micro-technologies are still largely proof-of-concept, and scalability and commercialization of micro-technologies will require increased accessibility to expensive equipment and resources, as well as simpler designs for usability. Here, we discuss three different miniaturized culturing practices; including microarrays, micromachined devices, and microfluidics; advancements to the field, and perceived challenges.
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Affiliation(s)
- Shanna-Leigh Davidson
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Tagbo H. R. Niepa
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA, United States
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, United States
- The McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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19
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Zhang P, Kaushik AM, Hsieh K, Li S, Lewis S, Mach KE, Liao JC, Carroll KC, Wang TH. A Cascaded Droplet Microfluidic Platform Enables High-Throughput Single Cell Antibiotic Susceptibility Testing at Scale. SMALL METHODS 2022; 6:e2101254. [PMID: 35041266 DOI: 10.1002/smtd.202101254] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Indexed: 06/14/2023]
Abstract
The global threat of antibiotic resistance underscores critical but unmet needs for rapid antibiotic susceptibility testing (AST) technologies. To this end, droplet microfluidic-based single-cell AST offers promise by achieving unprecedented rapidity, but its potential for clinical use is marred by the capacity of testing one to few antibiotic conditions per device, which falls short from the required scale in clinically relevant scenarios. To lift the scalability constraint in rapid single-cell AST technologies, a new cascaded droplet microfluidic platform that can streamline bacteria/antibiotic mixing, single-cell encapsulation within picoliter droplets, incubation, and detection in a continuous, assembly-line-like workflow is developed. The scalability of the platform is demonstrated by generating 32 groups of ≈10 000 droplets with custom antibiotic conditions within a single device, from which a new statistics-based method is used to analyze the single cell data and produce clinically useful antibiograms with minimum inhibitory concentrations in ≈90 min for the first antibiotic, plus 2 min for each subsequent antibiotic condition. Potential clinical utility of this platform is demonstrated by testing three clinical isolates and eight urine specimens against four frequently used antibiotics, and 100% and 93.8% categorical agreements are achieved compared to laboratory-based results that became available after 48 h.
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Affiliation(s)
- Pengfei Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Aniruddha M Kaushik
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Sixuan Li
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Shawna Lewis
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
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20
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Shin J, Shin S, Jung SH, Park C, Cho SY, Lee DG, Chung YJ. Duplex dPCR System for Rapid Identification of Gram-Negative Pathogens in the Blood of Patients with Bloodstream Infection: A Culture-Independent Approach. J Microbiol Biotechnol 2021; 31:1481-1489. [PMID: 34528911 PMCID: PMC9705831 DOI: 10.4014/jmb.2103.03044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/17/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
Early and accurate detection of pathogens is important to improve clinical outcomes of bloodstream infections (BSI), especially in the case of drug-resistant pathogens. In this study, we aimed to develop a culture-independent digital PCR (dPCR) system for multiplex detection of major sepsiscausing gram-negative pathogens and antimicrobial resistance genes using plasma DNA from BSI patients. Our duplex dPCR system successfully detected nine targets (five bacteria-specific targets and four antimicrobial resistance genes) through five reactions within 3 hours. The minimum detection limit was 50 ag of bacterial DNA, suggesting that 1 CFU/ml of bacteria in the blood can be detected. To validate the clinical applicability, cell-free DNA samples from febrile patients were tested with our system and confirmed high consistency with conventional blood culture. This system can support early identification of some drug-resistant gram-negative pathogens, which can help improving treatment outcomes of BSI.
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Affiliation(s)
- Juyoun Shin
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Sun Shin
- Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Seung-Hyun Jung
- Department of Biochemistry, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Yeun-Jun Chung
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Corresponding author Phone: +82-2-2258-7343 Fax: +82-2-537-0572 E-mail:
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21
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Sharaha U, Suleiman M, Abu-Aqil G, Riesenberg K, Lapidot I, Salman A, Huleihel M. Determination of Klebsiella pneumoniae Susceptibility to Antibiotics Using Infrared Microscopy. Anal Chem 2021; 93:13426-13433. [PMID: 34585907 DOI: 10.1021/acs.analchem.1c00734] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Klebsiella pneumoniae (K. pneumoniae) is one of the most aggressive multidrug-resistant bacteria associated with human infections, resulting in high mortality and morbidity. We obtained 1190 K. pneumoniae isolates from different patients with urinary tract infections. The isolates were measured to determine their susceptibility regarding nine specific antibiotics. This study's primary goal is to evaluate the potential of infrared spectroscopy in tandem with machine learning to assess the susceptibility of K. pneumoniae within approximately 20 min following the first culture. Our results confirm that it was possible to classify the isolates into sensitive and resistant with a success rate higher than 80% for the tested antibiotics. These results prove the promising potential of infrared spectroscopy as a powerful method for a K. pneumoniae susceptibility test.
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Affiliation(s)
- Uraib Sharaha
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Manal Suleiman
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - George Abu-Aqil
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | | | - Itshak Lapidot
- Department of Electrical and Electronics Engineering, ACLP-Afeka Center for Language Processing, Afeka Tel-Aviv Academic College of Engineering, Tel-Aviv 69107, Israel
| | - Ahmad Salman
- Department of Physics, SCE-Shamoon College of Engineering, Beer-Sheva 84100, Israel
| | - Mahmoud Huleihel
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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22
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Advances in Antimicrobial Resistance Monitoring Using Sensors and Biosensors: A Review. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9080232] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The indiscriminate use and mismanagement of antibiotics over the last eight decades have led to one of the main challenges humanity will have to face in the next twenty years in terms of public health and economy, i.e., antimicrobial resistance. One of the key approaches to tackling antimicrobial resistance is clinical, livestock, and environmental surveillance applying methods capable of effectively identifying antimicrobial non-susceptibility as well as genes that promote resistance. Current clinical laboratory practices involve conventional culture-based antibiotic susceptibility testing (AST) methods, taking over 24 h to find out which medication should be prescribed to treat the infection. Although there are techniques that provide rapid resistance detection, it is necessary to have new tools that are easy to operate, are robust, sensitive, specific, and inexpensive. Chemical sensors and biosensors are devices that could have the necessary characteristics for the rapid diagnosis of resistant microorganisms and could provide crucial information on the choice of antibiotic (or other antimicrobial medicines) to be administered. This review provides an overview on novel biosensing strategies for the phenotypic and genotypic determination of antimicrobial resistance and a perspective on the use of these tools in modern health-care and environmental surveillance.
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23
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Jeong Y, Jang H, Kang J, Nam J, Shin K, Kwon S, Choi J. Color-Coded Droplets and Microscopic Image Analysis for Multiplexed Antibiotic Susceptibility Testing. BIOSENSORS-BASEL 2021; 11:bios11080283. [PMID: 34436085 PMCID: PMC8393621 DOI: 10.3390/bios11080283] [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] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/16/2021] [Accepted: 08/16/2021] [Indexed: 01/11/2023]
Abstract
Since the discovery of antibiotics, the emergence of antibiotic resistance has become a global issue that is threatening society. In the era of antibiotic resistance, finding the proper antibiotics through antibiotic susceptibility testing (AST) is crucial in clinical settings. However, the current clinical process of AST based on the broth microdilution test has limitations on scalability to expand the number of antibiotics that are tested with various concentrations. Here, we used color-coded droplets to expand the multiplexing of AST regarding the kind and concentration of antibiotics. Color type and density differentiate the kind of antibiotics and concentration, respectively. Microscopic images of a large view field contain numbers of droplets with different testing conditions. Image processing analysis detects each droplet, decodes color codes, and measures the bacterial growth in the droplet. Testing E. coli ATCC 25922 with ampicillin, gentamicin, and tetracycline shows that the system can provide a robust and scalable platform for multiplexed AST. Furthermore, the system can be applied to various drug testing systems, which require several different testing conditions.
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Affiliation(s)
- Yunjin Jeong
- Bio-MAX Institute, Seoul National University, Seoul 08826, Korea;
| | - Haewook Jang
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Korea; (H.J.); (J.K.)
| | - Junwon Kang
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Korea; (H.J.); (J.K.)
- Integrated Major in Innovative Medical Science, Seoul National University, Seoul 03080, Korea
| | - Juhong Nam
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Korea; (J.N.); (K.S.)
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Korea; (J.N.); (K.S.)
| | - Sunghoon Kwon
- Bio-MAX Institute, Seoul National University, Seoul 08826, Korea;
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Korea; (H.J.); (J.K.)
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Korea; (J.N.); (K.S.)
- Institute of Entrepreneurial Bio Convergence, Seoul National University, Seoul 08826, Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea
- Center for Medical Institute, Seoul National University Hospital, Seoul 03080, Korea
- Correspondence: (S.K.); (J.C.)
| | - Jungil Choi
- School of Mechanical Engineering, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul 02707, Korea
- Correspondence: (S.K.); (J.C.)
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Acinetobacter baumannii: An Ancient Commensal with Weapons of a Pathogen. Pathogens 2021; 10:pathogens10040387. [PMID: 33804894 PMCID: PMC8063835 DOI: 10.3390/pathogens10040387] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter baumannii is regarded as a life-threatening pathogen associated with community-acquired and nosocomial infections, mainly pneumonia. The rise in the number of A. baumannii antibiotic-resistant strains reduces effective therapies and increases mortality. Bacterial comparative genomic studies have unraveled the innate and acquired virulence factors of A. baumannii. These virulence factors are involved in antibiotic resistance, environmental persistence, host-pathogen interactions, and immune evasion. Studies on host–pathogen interactions revealed that A. baumannii evolved different mechanisms to adhere to in order to invade host respiratory cells as well as evade the host immune system. In this review, we discuss current data on A. baumannii genetic features and virulence factors. An emphasis is given to the players in host–pathogen interaction in the respiratory tract. In addition, we report recent investigations into host defense systems using in vitro and in vivo models, providing new insights into the innate immune response to A. baumannii infections. Increasing our knowledge of A. baumannii pathogenesis may help the development of novel therapeutic strategies based on anti-adhesive, anti-virulence, and anti-cell to cell signaling pathways drugs.
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25
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Hwang JH, Lee SY, Choi J. Microscopic Analysis of Bacterial Inoculum Effect Using Micropatterned Biochip. Antibiotics (Basel) 2021; 10:antibiotics10030300. [PMID: 33805824 PMCID: PMC7998646 DOI: 10.3390/antibiotics10030300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/05/2022] Open
Abstract
Antimicrobial resistance has become a major problem in public health and clinical environments. Against this background, antibiotic susceptibility testing (AST) has become necessary to cure diseases in an appropriate and timely manner as it indicates the necessary concentration of antibiotics. Recently, microfluidic based rapid AST methods using microscopic analysis have been shown to reduce the time needed for the determination of the proper antibiotics. However, owing to the inoculum effect, the accurate measurement of the minimal inhibitory concentration (MIC) is difficult. We tested four standard bacteria: Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, and Enterococcus faecalis, against five different antibiotics: piperacillin, cefotaxime, amikacin, levofloxacin, and ampicillin. The results showed that overall, the microfluidic system has a similar inoculum effect compared to the conventional AST method. However, due to the different testing conditions and determination protocols of the growth of the microfluidic based rapid AST, a few results are not identical to the conventional methods using optical density. This result suggests that microfluidic based rapid AST methods require further research on the inoculum effect for practical use in hospitals and can then be used for effective antibiotic prescriptions.
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Affiliation(s)
- Jung Ho Hwang
- Department of Electrical and Computer Engineering, Undergraduate School, Michigan State University, 426 Auditorium Road, East Lansing, MI 48824, USA;
| | - Sang Young Lee
- Department of Mechanical Engineering, Undergraduate School, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul 02707, Korea;
| | - Jungil Choi
- School of Mechanical Engineering, Kookmin University, 77 Jeongneung-ro, Seongbuk-gu, Seoul 02707, Korea
- Correspondence: ; Tel.: +82-2-910-4684
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26
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Kost GJ. Geospatial Spread of Antimicrobial Resistance, Bacterial and Fungal Threats to Coronavirus Infectious Disease 2019 (COVID-19) Survival, and Point-of-Care Solutions. Arch Pathol Lab Med 2021; 145:145-167. [PMID: 32886738 DOI: 10.5858/arpa.2020-0284-ra] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/15/2022]
Abstract
CONTEXT.— Point-of-care testing (POCT) is inherently spatial, that is, performed where needed, and intrinsically temporal, because it accelerates decision-making. POCT efficiency and effectiveness have the potential to facilitate antimicrobial resistance (AMR) detection, decrease risks of coinfections for critically ill patients with coronavirus infectious disease 2019 (COVID-19), and improve the cost-effectiveness of health care. OBJECTIVES.— To assess AMR identification by using POCT, describe the United States AMR Diagnostic Challenge, and improve global standards of care for infectious diseases. DATA SOURCES.— PubMed, World Wide Web, and other sources were searched for papers focusing on AMR and POCT. EndNote X9.1 (Clarivate Analytics) consolidated abstracts, URLs, and PDFs representing approximately 500 articles were assessed for relevance. Panelist insights at Tri•Con 2020 in San Francisco and finalist POC technologies competing for a US $20,000,000 AMR prize are summarized. CONCLUSIONS.— Coinfections represent high risks for COVID-19 patients. POCT potentially will help target specific pathogens, refine choices for antimicrobial drugs, and prevent excess morbidity and mortality. POC assays that identify patterns of pathogen resistance can help tell us how infected individuals spread AMR, where geospatial hotspots are located, when delays cause death, and how to deploy preventative resources. Shared AMR data "clouds" could help reduce critical care burden during pandemics and optimize therapeutic options, similar to use of antibiograms in individual hospitals. Multidisciplinary health care personnel should learn the principles and practice of POCT, so they can meet needs with rapid diagnostic testing. The stakes are high. Antimicrobial resistance is projected to cause millions of deaths annually and cumulative financial loses in the trillions by 2050.
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Affiliation(s)
- Gerald J Kost
- From Knowledge Optimization, Davis, California; and Point-of-Care Testing Center for Teaching and Research (POCT•CTR), University of California, Davis
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27
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Chow EKH. The 2020 SLAS Technology Top Ten: Translating Life Sciences Innovation. SLAS Technol 2021; 26:37-41. [PMID: 33482077 DOI: 10.1177/2472630320982580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Rentschler S, Kaiser L, Deigner HP. Emerging Options for the Diagnosis of Bacterial Infections and the Characterization of Antimicrobial Resistance. Int J Mol Sci 2021; 22:E456. [PMID: 33466437 PMCID: PMC7796476 DOI: 10.3390/ijms22010456] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 02/06/2023] Open
Abstract
Precise and rapid identification and characterization of pathogens and antimicrobial resistance patterns are critical for the adequate treatment of infections, which represent an increasing problem in intensive care medicine. The current situation remains far from satisfactory in terms of turnaround times and overall efficacy. Application of an ineffective antimicrobial agent or the unnecessary use of broad-spectrum antibiotics worsens the patient prognosis and further accelerates the generation of resistant mutants. Here, we provide an overview that includes an evaluation and comparison of existing tools used to diagnose bacterial infections, together with a consideration of the underlying molecular principles and technologies. Special emphasis is placed on emerging developments that may lead to significant improvements in point of care detection and diagnosis of multi-resistant pathogens, and new directions that may be used to guide antibiotic therapy.
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Affiliation(s)
- Simone Rentschler
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 VS-Schwenningen, Germany; (S.R.); (L.K.)
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Lars Kaiser
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 VS-Schwenningen, Germany; (S.R.); (L.K.)
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg i. Br., Germany
| | - Hans-Peter Deigner
- Institute of Precision Medicine, Furtwangen University, Jakob-Kienzle-Straße 17, 78054 VS-Schwenningen, Germany; (S.R.); (L.K.)
- EXIM Department, Fraunhofer Institute IZI (Leipzig), Schillingallee 68, 18057 Rostock, Germany
- Faculty of Science, Tuebingen University, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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29
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Aloni-Grinstein R, Shifman O, Gur D, Aftalion M, Rotem S. MAPt: A Rapid Antibiotic Susceptibility Testing for Bacteria in Environmental Samples as a Means for Bioterror Preparedness. Front Microbiol 2020; 11:592194. [PMID: 33224128 PMCID: PMC7674193 DOI: 10.3389/fmicb.2020.592194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/30/2020] [Indexed: 12/24/2022] Open
Abstract
Antibiotic resistance of bio-threat agents holds major concerns especially in light of advances in methods for engineering pathogens with antibiotic resistance. Preparedness means for rapid identification and prompt proper medical treatment are of need to contain the event and prevent morbidity and spreading of the disease by properly treating exposed individuals before symptoms appearance. Herein, we describe a novel, rapid, simple, specific, and sensitive method named Micro-Agar-PCR-test (MAPt), which determines antibiotic susceptibility of bio-terror pathogens, directly from environmental samples, with no need for any prior isolation, quantification, or enrichment steps. As proof of concept, we have used this approach to obtain correct therapeutic antibiotic minimal inhibitory concentration (MIC) values for the Tier-1 select agents, Bacillus anthracis, Yersinia pestis, and Francisella tularensis, spiked in various environmental samples recapitulating potential bioterror scenarios. The method demonstrated efficiency for a broad dynamic range of bacterial concentrations, both for fast-growing as well as slow-growing bacteria and most importantly significantly shortening the time for accurate results from days to a few hours. The MAPt allows us to address bioterror agents-contaminated environmental samples, offering rational targeted prophylactic treatment, before the onset of morbidity in exposed individuals. Hence, MAPt is expected to provide data for decision-making personal for treatment regimens before the onset of symptoms in infected individuals.
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Affiliation(s)
- Ronit Aloni-Grinstein
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Ohad Shifman
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - David Gur
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Moshe Aftalion
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
| | - Shahar Rotem
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness-Ziona, Israel
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30
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Åkerlund A, Jonasson E, Matuschek E, Serrander L, Sundqvist M, Kahlmeter G. EUCAST rapid antimicrobial susceptibility testing (RAST) in blood cultures: validation in 55 European laboratories. J Antimicrob Chemother 2020; 75:3230-3238. [PMID: 32789506 PMCID: PMC7566356 DOI: 10.1093/jac/dkaa333] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/26/2020] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES When bloodstream infections are caused by resistant bacteria, rapid antimicrobial susceptibility testing (RAST) is important for adjustment of therapy. The EUCAST RAST method, directly from positive blood cultures, was validated in a multi-laboratory study in Europe. METHODS RAST was performed in 40 laboratories in northern Europe (NE) and 15 in southern Europe (SE) from clinical blood cultures positive for Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus or Streptococcus pneumoniae. Categorical results at 4, 6 and 8 h of incubation were compared with results for EUCAST standard 16-20 h disc diffusion. The method, preliminary breakpoints and the performance of the laboratories were evaluated. RESULTS The total number of isolates was 833/318 in NE/SE. The number of zone diameters that could be read (88%, 96% and 99%) and interpreted (70%, 81% and 85%) increased with incubation time (4, 6 and 8 h). The categorical agreement was acceptable, with total error rates in NE/SE of 2.4%/4.9% at 4 h, 1.1%/3.5% at 6 h and 1.1%/3.3% at 8 h. False susceptibility at 4, 6 and 8 h of incubation was below 0.3% and 1.1% in NE and SE, respectively, and the corresponding percentages for false resistance were below 1.9% and 2.8%. After fine-tuning breakpoints, more zones could be interpreted (73%, 89% and 93%), with only marginally affected error rates. CONCLUSIONS The EUCAST RAST method can be implemented in routine laboratories without major investments. It provides reliable antimicrobial susceptibility testing results for relevant bloodstream infection pathogens after 4-6 h of incubation.
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Affiliation(s)
- Anna Åkerlund
- Division of Clinical Microbiology, County Hospital Ryhov, Jönköping, Sweden
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Division of Clinical Microbiology, Linköping University Hospital, Linköping, Sweden
| | - Emma Jonasson
- Department of Clinical Microbiology, Central Hospital, Växjö, Sweden
- EUCAST Development Laboratory, Växjö, Sweden
| | | | - Lena Serrander
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Division of Clinical Microbiology, Linköping University Hospital, Linköping, Sweden
| | - Martin Sundqvist
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Gunnar Kahlmeter
- Department of Clinical Microbiology, Central Hospital, Växjö, Sweden
- EUCAST Development Laboratory, Växjö, Sweden
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31
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Spencer DC, Paton TF, Mulroney KT, Inglis TJJ, Sutton JM, Morgan H. A fast impedance-based antimicrobial susceptibility test. Nat Commun 2020; 11:5328. [PMID: 33087704 PMCID: PMC7578651 DOI: 10.1038/s41467-020-18902-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to develop simple and fast antimicrobial susceptibility tests (ASTs) that allow informed prescribing of antibiotics. Here, we describe a label-free AST that can deliver results within an hour, using an actively dividing culture as starting material. The bacteria are incubated in the presence of an antibiotic for 30 min, and then approximately 105 cells are analysed one-by-one with microfluidic impedance cytometry for 2-3 min. The measured electrical characteristics reflect the phenotypic response of the bacteria to the mode of action of a particular antibiotic, in a 30-minute incubation window. The results are consistent with those obtained by classical broth microdilution assays for a range of antibiotics and bacterial species.
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Affiliation(s)
- Daniel C Spencer
- Department of Electronics and Computer Science, and Institute for Life Science, University of Southampton, Hampshire, SO17 1BJ, UK
| | - Teagan F Paton
- Department of Microbiology, PathWest Laboratory Medicine, Nedlands, WA, 6009, Australia
| | - Kieran T Mulroney
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
| | - Timothy J J Inglis
- Department of Microbiology, PathWest Laboratory Medicine, Nedlands, WA, 6009, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
| | - J Mark Sutton
- Public Health England, National Infection Service, Porton Down, Salisbury, Wiltshire, SP4 0JG, UK
| | - Hywel Morgan
- Department of Electronics and Computer Science, and Institute for Life Science, University of Southampton, Hampshire, SO17 1BJ, UK.
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32
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Bagudo AI, Obande GA, Harun A, Singh KKB. Advances in automated techniques to identify Acinetobacter calcoaceticus-Acinetobacter baumannii complex. ASIAN BIOMED 2020; 14:177-186. [PMID: 37551265 PMCID: PMC10373397 DOI: 10.1515/abm-2020-0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Acinetobacter species, particularly those within Acinetobacter calcoaceticus-A. baumannii complex (ACB complex), have emerged as clinically relevant pathogens in hospital environments worldwide. Early and quick detection and identification of Acinetobacter infections is challenging, and traditional culture and biochemical methods may not achieve adequate levels of speciation. Moreover, currently available techniques to identify and differentiate closely related Acinetobacter species are insufficient. The objective of this review is to recapitulate the current evolution in phenotypic and automated techniques used to identify the ACB complex. Compared with other automated or semiautomated systems of bacterial identification, matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) demonstrates a high level of Acinetobacter species identification and discrimination, including newly discovered species A. seifertii and A. dijkshoorniae.
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Affiliation(s)
- Ahmad Ibrahim Bagudo
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
| | - Godwin Attah Obande
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
| | - Kirnpal Kaur Banga Singh
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150Kubang Kerian, Kelantan, Malaysia
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33
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Shanmugakani RK, Srinivasan B, Glesby MJ, Westblade LF, Cárdenas WB, Raj T, Erickson D, Mehta S. Current state of the art in rapid diagnostics for antimicrobial resistance. LAB ON A CHIP 2020; 20:2607-2625. [PMID: 32644060 PMCID: PMC7428068 DOI: 10.1039/d0lc00034e] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Antimicrobial resistance (AMR) is a fundamental global concern analogous to climate change threatening both public health and global development progress. Infections caused by antimicrobial-resistant pathogens pose serious threats to healthcare and human capital. If the increasing rate of AMR is left uncontrolled, it is estimated that it will lead to 10 million deaths annually by 2050. This global epidemic of AMR necessitates radical interdisciplinary solutions to better detect antimicrobial susceptibility and manage infections. Rapid diagnostics that can identify antimicrobial-resistant pathogens to assist clinicians and health workers in initiating appropriate treatment are critical for antimicrobial stewardship. In this review, we summarize different technologies applied for the development of rapid diagnostics for AMR and antimicrobial susceptibility testing (AST). We briefly describe the single-cell technologies that were developed to hasten the AST of infectious pathogens. Then, the different types of genotypic and phenotypic techniques and the commercially available rapid diagnostics for AMR are discussed in detail. We conclude by addressing the potential of current rapid diagnostic systems being developed as point-of-care (POC) diagnostic tools and the challenges to adapt them at the POC level. Overall, this review provides an insight into the current status of rapid and POC diagnostic systems for AMR.
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Affiliation(s)
- Rathina Kumar Shanmugakani
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Balaji Srinivasan
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
| | - Marshall J. Glesby
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F. Westblade
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Washington B. Cárdenas
- Laboratorio para Investigaciones Biomédicas, Escuela Superior Politécnica del Litoral, Guayaquil, Guayas, Ecuador
| | - Tony Raj
- St. John’s Research Institute, Bangalore, Karnataka, India
| | - David Erickson
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
| | - Saurabh Mehta
- Institute for Nutritional Sciences, Global Health, and Technology, Cornell University, Ithaca, New York, USA
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, USA
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34
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Hedde PN, Bouzin M, Abram TJ, Chen X, Toosky MN, Vu T, Li Y, Zhao W, Gratton E. Rapid isolation of rare targets from large fluid volumes. Sci Rep 2020; 10:12458. [PMID: 32719382 PMCID: PMC7385493 DOI: 10.1038/s41598-020-69315-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/26/2020] [Indexed: 11/24/2022] Open
Abstract
Rapidly isolating rare targets from larger, clinically relevant fluid volumes remains an unresolved problem in biomedicine and diagnosis. Here, we describe how 3D particle sorting can enrich targets at ultralow concentrations over 100-fold within minutes not possible with conventional approaches. Current clinical devices based on biochemical extraction and microfluidic solutions typically require high concentrations and/or can only process sub-milliliter volumes in time. In a proof-of-concept application, we isolated bacteria from whole blood as demanded for rapid sepsis diagnosis where minimal numbers of bacteria need to be found in a 1–10 mL blood sample. After sample encapsulation in droplets and target enrichment with the 3D particle sorter within a few minutes, downstream analyses were able to identify bacteria and test for antibiotic susceptibility, information which is critical for successful treatment of bloodstream infections.
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Affiliation(s)
- Per Niklas Hedde
- Department of Biomedical Engineering, University of California, Irvine, CA, USA. .,Department of Biochemistry, University of Hawaii at Manoa, Manoa, HI, USA.
| | - Margaux Bouzin
- Department of Biomedical Engineering, University of California, Irvine, CA, USA.,Physics Department, Università degli Studi di Milano-Bicocca, Milan, Italy
| | | | - Xiaoming Chen
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | | | - Tam Vu
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Yiyan Li
- Department of Physics and Engineering, Fort Lewis College, Durango, CO, USA
| | - Weian Zhao
- Department of Biomedical Engineering, University of California, Irvine, CA, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA.,Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA.,Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA.,Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, USA.,Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, CA, USA
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35
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Vasala A, Hytönen VP, Laitinen OH. Modern Tools for Rapid Diagnostics of Antimicrobial Resistance. Front Cell Infect Microbiol 2020; 10:308. [PMID: 32760676 PMCID: PMC7373752 DOI: 10.3389/fcimb.2020.00308] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/22/2020] [Indexed: 12/18/2022] Open
Abstract
Fast, robust, and affordable antimicrobial susceptibility testing (AST) is required, as roughly 50% of antibiotic treatments are started with wrong antibiotics and without a proper diagnosis of the pathogen. Validated growth-based AST according to EUCAST or CLSI (European Committee on Antimicrobial Susceptibility Testing, Clinical Laboratory Standards Institute) recommendations is currently suggested to guide the antimicrobial therapy. Any new AST should be validated against these standard methods. Many rapid diagnostic techniques can already provide pathogen identification. Some of them can additionally detect the presence of resistance genes or resistance proteins, but usually isolated pure cultures are needed for AST. We discuss the value of the technologies applying nucleic acid amplification, whole genome sequencing, and hybridization as well as immunodiagnostic and mass spectrometry-based methods and biosensor-based AST. Additionally, we evaluate the potential of integrated systems applying microfluidics to integrate cultivation, lysis, purification, and signal reading steps. We discuss technologies and commercial products with potential for Point-of-Care Testing (POCT) and their capability to analyze polymicrobial samples without pre-purification steps. The purpose of this critical review is to present the needs and drivers for AST development, to show the benefits and limitations of AST methods, to introduce promising new POCT-compatible technologies, and to discuss AST technologies that are likely to thrive in the future.
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Affiliation(s)
- Antti Vasala
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vesa P. Hytönen
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
| | - Olli H. Laitinen
- Protein Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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Dietvorst J, Vilaplana L, Uria N, Marco MP, Muñoz-Berbel X. Current and near-future technologies for antibiotic susceptibility testing and resistant bacteria detection. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115891] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing. Sci Rep 2020; 10:7622. [PMID: 32376847 PMCID: PMC7203151 DOI: 10.1038/s41598-020-64616-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/20/2020] [Indexed: 12/27/2022] Open
Abstract
Bloodstream infections (BSI) and sepsis are major causes of morbidity and mortality worldwide. Blood culture-based diagnostics usually requires 1-2 days for identification of bacterial agent and an additional 2-3 days for phenotypic determination of antibiotic susceptibility pattern. With the escalating burden of antimicrobial resistance (AMR) rapid diagnostics becomes increasingly important to secure adequate antibiotic therapy. Real-time whole genome sequencing represents a genotypic diagnostic approach with the ability to rapidly identify pathogens and AMR-encoding genes. Here we have used nanopore sequencing of bacterial DNA extracted from positive blood cultures for identification of pathogens, detection of plasmids and AMR-encoding genes. To our knowledge, this is the first study to gather the above-mentioned information from nanopore sequencing and conduct a comprehensive analysis for diagnostic purposes in real-time. Identification of pathogens was possible after 10 minutes of sequencing and all predefined AMR-encoding genes and plasmids from monoculture experiments were detected within one hour using raw nanopore sequencing data. Furthermore, we demonstrate the correct identification of plasmids and blaCTX-M subtypes using de novo assembled nanopore contigs. Results from this study hold great promise for future applications in clinical microbiology and for health care surveillance purposes.
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Ma L, Petersen M, Lu X. Identification and Antimicrobial Susceptibility Testing of Campylobacter Using a Microfluidic Lab-on-a-Chip Device. Appl Environ Microbiol 2020; 86:e00096-20. [PMID: 32111591 PMCID: PMC7170473 DOI: 10.1128/aem.00096-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 02/22/2020] [Indexed: 01/14/2023] Open
Abstract
Campylobacter spp. have been recognized as major foodborne pathogens worldwide. An increasing frequency of antibiotic-resistant pathogens, including Campylobacter spp., have been identified to transmit from food products to humans and cause severe threats to public health. To better mitigate the antibiotic resistance crisis, rapid detection methods are required to provide timely antimicrobial resistance surveillance data for agri-food systems. Herein, we developed a polymer-based microfluidic device for the identification and antimicrobial susceptibility testing (AST) of Campylobacter spp. An array of bacterial incubation chambers were created in the microfluidic device, where chromogenic medium and antibiotics were loaded. The growth of Campylobacter spp. was visualized by color change due to chromogenic reactions. This platform achieved 100% specificity for Campylobacter identification. Sensitive detection of multiple Campylobacter species (C. jejuni, C. coli, and C. lari) was obtained in artificially contaminated milk and poultry meat, with detection limits down to 1 × 102 CFU/ml and 1 × 104 CFU/25 g, respectively. On-chip AST determined Campylobacter antibiotic susceptibilities by the lowest concentration of antibiotics that can inhibit bacterial growth (i.e., no color change observed). High coincidences (91% to 100%) of on-chip AST and the conventional agar dilution method were achieved against several clinically important antibiotics. For a presumptive colony, on-chip identification and AST were completed in parallel within 24 h, whereas standard methods, including biochemical assays and traditional culture-based AST, take several days for multiple sequential steps. In conclusion, this lab-on-a-chip device can achieve rapid and reliable detection of antibiotic-resistant Campylobacter spp.IMPORTANCE Increasing concerns of antibiotic-resistant Campylobacter spp. with regard to public health emphasize the importance of efficient and fast detection. This study described the timely identification and antimicrobial susceptibility testing of Campylobacter spp. by using a microfluidic device. Our developed method not only reduced the total analysis time, but it also simplified food sample preparation and chip operation for end users. Due to the miniaturized size of the lab-on-a-chip platform, the detection was achieved by using up to 1,000 times less of the reagents than with standard reference methods, making it a competitive approach for rapid screening and surveillance study in food industries. In addition, multiple clinically important Campylobacter species (C. jejuni, C. coli, and C. lari) could be tested by our device. This device has potential for wide application in food safety management and clinical diagnostics, especially in resource-limited regions.
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Affiliation(s)
- Luyao Ma
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Marlen Petersen
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
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Zhang K, Qin S, Wu S, Liang Y, Li J. Microfluidic systems for rapid antibiotic susceptibility tests (ASTs) at the single-cell level. Chem Sci 2020; 11:6352-6361. [PMID: 34094102 PMCID: PMC8159419 DOI: 10.1039/d0sc01353f] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Infectious diseases caused by multidrug resistant (MDR) bacterial pathogens are impending threats to global health. Since delays in identifying drug resistance would significantly increase mortality, fast and accurate antibiotic susceptibility tests (ASTs) are critical for addressing the antibiotic resistance issue. However, the conventional methods for ASTs are always labor-intensive, imprecise, complex and slow (taking 2-3 days). To address these issues, some advanced microfluidic systems have been designed for rapid phenotypic and genotypic analysis of antibiotic resistance. This review highlights the recent development of microfluidics-based ASTs at the single-cell or single-molecule level for guiding antibiotic treatment decisions and predicting therapeutic outcomes.
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Affiliation(s)
- Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
| | - Sixuan Wu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
| | - Yan Liang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University Zhengzhou 450001 China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
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Ayoub Moubareck C, Hammoudi Halat D. Insights into Acinetobacter baumannii: A Review of Microbiological, Virulence, and Resistance Traits in a Threatening Nosocomial Pathogen. Antibiotics (Basel) 2020; 9:antibiotics9030119. [PMID: 32178356 PMCID: PMC7148516 DOI: 10.3390/antibiotics9030119] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Being a multidrug-resistant and an invasive pathogen, Acinetobacter baumannii is one of the major causes of nosocomial infections in the current healthcare system. It has been recognized as an agent of pneumonia, septicemia, meningitis, urinary tract and wound infections, and is associated with high mortality. Pathogenesis in A. baumannii infections is an outcome of multiple virulence factors, including porins, capsules, and cell wall lipopolysaccharide, enzymes, biofilm production, motility, and iron-acquisition systems, among others. Such virulence factors help the organism to resist stressful environmental conditions and enable development of severe infections. Parallel to increased prevalence of infections caused by A. baumannii, challenging and diverse resistance mechanisms in this pathogen are well recognized, with major classes of antibiotics becoming minimally effective. Through a wide array of antibiotic-hydrolyzing enzymes, efflux pump changes, impermeability, and antibiotic target mutations, A. baumannii models a unique ability to maintain a multidrug-resistant phenotype, further complicating treatment. Understanding mechanisms behind diseases, virulence, and resistance acquisition are central to infectious disease knowledge about A. baumannii. The aims of this review are to highlight infections and disease-producing factors in A. baumannii and to touch base on mechanisms of resistance to various antibiotic classes.
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Affiliation(s)
- Carole Ayoub Moubareck
- College of Natural and Health Sciences, Zayed University, Dubai P.O. Box 144534, UAE
- Correspondence: ; Tel.: +971-4-402-1745
| | - Dalal Hammoudi Halat
- Department of Pharmaceutical Sciences, School of Pharmacy, Lebanese International University, Beirut, Bekaa Campuses 1103, Lebanon;
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41
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Clinical impact of rapid susceptibility testing on Mueller-Hinton Rapid-SIR directly from urine specimens. Eur J Clin Microbiol Infect Dis 2020; 39:1373-1377. [PMID: 32090300 DOI: 10.1007/s10096-020-03855-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/17/2020] [Indexed: 10/23/2022]
Abstract
Urinary tract infection diagnosis and management generally involves a 48-h microbiological delay to obtain the antibiotic susceptibility test (AST) results. In the context of multidrug resistance, reducing the time to obtain AST results is an essential factor, allowing for more timely appropriate treatment. We conducted a single-centre prospective study on urinary samples meeting two criteria: significant leukocyturia > 50/mm3 and exclusive presence of Gram-negative bacilli on direct examination. AST were performed by direct inoculation on Mueller-Hinton Rapid-SIR (MHR-SIR) agar. We evaluated the time to antibiotic adaptation by the antimicrobial stewardship team according to rapid AST results. Patients were subsequently excluded from the study if asymptomatic bacteria were confirmed, or in the absence of clinical data. Seventy patients were included. Mean age of patients was 68.8 years (± 21.3). Empirical antibiotic treatment were mainly based on third generation cephalosporins (n = 33), fluoroquinolones (n = 15), beta-lactamin/beta-lactamase inhibitors (n = 7), fosfomycin and nitrofurantoin (n = 5, each). The average time to obtain results was 7.2 h (± 1.6 h). Adaptation of therapy following MHR-SIR was performed for 29 patients (41%) with early switch to oral antibiotics, de-escalation or escalation in respectively 72.3%, 30%, and 11% of cases. Time saving of MHR-SIR compared with the standard technique was 42.6 (± 16.7) h. This study showed that rapid antibiotic susceptibility test results, using MHR-SIR method directly from urine, can be obtained 40 h earlier than conventional AST. The study also demonstrated significant clinical impact on the selection and reduction of the antibiotic therapy spectrum.
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Abram TJ, Cherukury H, Ou CY, Vu T, Toledano M, Li Y, Grunwald JT, Toosky MN, Tifrea DF, Slepenkin A, Chong J, Kong L, Del Pozo DV, La KT, Labanieh L, Zimak J, Shen B, Huang SS, Gratton E, Peterson EM, Zhao W. Rapid bacterial detection and antibiotic susceptibility testing in whole blood using one-step, high throughput blood digital PCR. LAB ON A CHIP 2020; 20:477-489. [PMID: 31872202 PMCID: PMC7250044 DOI: 10.1039/c9lc01212e] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Sepsis due to antimicrobial resistant pathogens is a major health problem worldwide. The inability to rapidly detect and thus treat bacteria with appropriate agents in the early stages of infections leads to excess morbidity, mortality, and healthcare costs. Here we report a rapid diagnostic platform that integrates a novel one-step blood droplet digital PCR assay and a high throughput 3D particle counter system with potential to perform bacterial identification and antibiotic susceptibility profiling directly from whole blood specimens, without requiring culture and sample processing steps. Using CTX-M-9 family ESBLs as a model system, we demonstrated that our technology can simultaneously achieve unprecedented high sensitivity (10 CFU per ml) and rapid sample-to-answer assay time (one hour). In head-to-head studies, by contrast, real time PCR and BioRad ddPCR only exhibited a limit of detection of 1000 CFU per ml and 50-100 CFU per ml, respectively. In a blinded test inoculating clinical isolates into whole blood, we demonstrated 100% sensitivity and specificity in identifying pathogens carrying a particular resistance gene. We further demonstrated that our technology can be broadly applicable for targeted detection of a wide range of antibiotic resistant genes found in both Gram-positive (vanA, nuc, and mecA) and Gram-negative bacteria, including ESBLs (blaCTX-M-1 and blaCTX-M-2 families) and CREs (blaOXA-48 and blaKPC), as well as bacterial speciation (E. coli and Klebsiella spp.) and pan-bacterial detection, without requiring blood culture or sample processing. Our rapid diagnostic technology holds great potential in directing early, appropriate therapy and improved antibiotic stewardship in combating bloodstream infections and antibiotic resistance.
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Affiliation(s)
- Timothy J Abram
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA.
| | - Hemanth Cherukury
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA. and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Chen-Yin Ou
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA.
| | - Tam Vu
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA. and Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Michael Toledano
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Yiyan Li
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA. and Department of Physics and Engineering, Fort Lewis College, Durango, CO 81301, USA
| | | | - Melody N Toosky
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA.
| | - Delia F Tifrea
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Anatoly Slepenkin
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Jonathan Chong
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Lingshun Kong
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Domenica Vanessa Del Pozo
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Kieu Thai La
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Louai Labanieh
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Jan Zimak
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Byron Shen
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA.
| | - Susan S Huang
- Division of Infectious Diseases, UCI School of Medicine, Irvine, CA 92697, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA and Laboratory for Fluorescence Dynamics, University of California, Irvine, CA 92697, USA
| | - Ellena M Peterson
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA. and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA and Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA and Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA and Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, USA and Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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43
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Scholtzek AD, Hanke D, Eichhorn I, Walther B, Lübke-Becker A, van Duijkeren E, Köck R, Schwarz S, Feßler AT. Heterogeneity of antimicrobial susceptibility testing results for sulfamethoxazole/trimethoprim obtained from clinical equine Staphylococcus aureus isolates using different methods. Vet Microbiol 2020; 242:108600. [PMID: 32122605 DOI: 10.1016/j.vetmic.2020.108600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/21/2020] [Accepted: 01/30/2020] [Indexed: 11/25/2022]
Abstract
Based on antimicrobial susceptibility testing (AST), correct classifications as susceptible, intermediate or resistant are challenging for some antimicrobial agent-bacterial species combinations. In this study, we investigated 19 equine Staphylococcus aureus isolates for their susceptibility to the combination sulfamethoxazole/trimethoprim (SXT) by using broth microdilution (BMD), agar disk diffusion (DD) and automated test systems. To elucidate the presence of the corresponding genetic resistance properties among the isolates, whole genome sequence analysis was performed and the genomes were screened for trimethoprim (TMP) resistance genes and mutations in the deduced FolP amino acid (aa) sequences, known to confer sulfonamide resistance. To check for hetero-resistance, zone diameters in DD were screened after 18 and 42 h of incubation. All 19 isolates harboured one of the TMP resistance genes dfrG or dfrS1. Three isolates had an aa exchange in their FolP aa sequence (F17L), which has previously been described to result in sulfonamide resistance. These isolates were classified as SXT-resistant by all methods. The remaining 16 isolates were classified as SXT-susceptible or -intermediate (BMD and/or DD) or SXT-resistant (mainly automated test systems). None of the isolates had relevant aa variations in their FolP aa sequences. All 19 isolates showed slight growth within their SXT inhibition zone by DD, pointing towards hetero-resistance. Overall, automated test systems classified isolates lacking genetic resistance determinants more frequently as SXT-resistant than DD and BMD. Therefore, further studies are needed to define a reliable method for SXT susceptibility testing.
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Affiliation(s)
- Anissa D Scholtzek
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Dennis Hanke
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Inga Eichhorn
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Birgit Walther
- Advanced Light and Electron Microscopy (ZBS-4), Robert Koch Institute, Berlin, Germany
| | - Antina Lübke-Becker
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Engeline van Duijkeren
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control (CIb), Bilthoven, the Netherlands
| | - Robin Köck
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany; Institute of Hygiene, DRK Kliniken Berlin, Berlin, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Andrea T Feßler
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.
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Hong JS, Kim D, Kang DY, Park BY, Yang S, Yoon EJ, Lee H, Jeong SH. Evaluation of the BD Phoenix M50 Automated Microbiology System for Antimicrobial Susceptibility Testing with Clinical Isolates in Korea. Microb Drug Resist 2019; 25:1142-1148. [DOI: 10.1089/mdr.2018.0370] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Jun Sung Hong
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul, Korea
| | - Dokyun Kim
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul, Korea
| | - Da Young Kang
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul, Korea
| | - Byeol Yi Park
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul, Korea
| | - SunMi Yang
- Division of Diagnostic Systems, BD Life Science, Seoul, Korea
| | - Eun-Jung Yoon
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul, Korea
| | - Hyukmin Lee
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul, Korea
| | - Seok Hoon Jeong
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, College of Medicine, Yonsei University, Seoul, Korea
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45
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Abstract
Acinetobacter species have emerged as one of the most clinically important pathogens. The phenotypic techniques which are currently available are insufficient in accurately identifying and differentiating the closely related and clinically important Acinetobacter species. Here, we discuss the advantages and limitations of the conventional phenotypic methods, automated identification systems, molecular methods and MALDI-TOF in the precise identification and differentiation of Acinetobacter species. More specifically, several species of this genus are increasingly reported to be of high clinical importance. Molecular characterization such as of blaOXA-51-like PCR together with rpoB sequencing has high discriminatory power over the conventional methods for Acinetobacter species identification, especially within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex. Acinetobacter species are considered to be one of the most important pathogens and associated with increased mortality. The species within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex have emerged as high priority pathogens, especially in intensive care units, thereby posing a challenge to infection management practices. However, identification of Acinetobacter to the species level is difficult. Clear differentiation among various Acinetobacter species with available standard biochemical methods and automated systems is challenging. Although various molecular methods are available, they are not regularly used in diagnostic laboratories. The advantages and disadvantages of different methods useful in the accurate identification of Acinetobacter species are discussed in this review.
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46
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Shin DJ, Andini N, Hsieh K, Yang S, Wang TH. Emerging Analytical Techniques for Rapid Pathogen Identification and Susceptibility Testing. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:41-67. [PMID: 30939033 PMCID: PMC7369001 DOI: 10.1146/annurev-anchem-061318-115529] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In the face of looming threats from multi-drug resistant microorganisms, there is a growing need for technologies that will enable rapid identification and drug susceptibility profiling of these pathogens in health care settings. In particular, recent progress in microfluidics and nucleic acid amplification is pushing the boundaries of timescale for diagnosing bacterial infections. With a diverse range of techniques and parallel developments in the field of analytical chemistry, an integrative perspective is needed to understand the significance of these developments. This review examines the scope of new developments in assay technologies grouped by key enabling domains of research. First, we examine recent development in nucleic acid amplification assays for rapid identification and drug susceptibility testing in bacterial infections. Next, we examine advances in microfluidics that facilitate acceleration of diagnostic assays via integration and scale. Lastly, recentdevelopments in biosensor technologies are reviewed. We conclude this review with perspectives on the use of emerging concepts to develop paradigm-changing assays.
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Affiliation(s)
- Dong Jin Shin
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Nadya Andini
- Department of Emergency Medicine, Stanford University, Stanford, California 94305, USA;
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Samuel Yang
- Department of Emergency Medicine, Stanford University, Stanford, California 94305, USA;
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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47
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Adaptable microfluidic system for single-cell pathogen classification and antimicrobial susceptibility testing. Proc Natl Acad Sci U S A 2019; 116:10270-10279. [PMID: 31068473 DOI: 10.1073/pnas.1819569116] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Infectious diseases caused by bacterial pathogens remain one of the most common causes of morbidity and mortality worldwide. Rapid microbiological analysis is required for prompt treatment of bacterial infections and to facilitate antibiotic stewardship. This study reports an adaptable microfluidic system for rapid pathogen classification and antimicrobial susceptibility testing (AST) at the single-cell level. By incorporating tunable microfluidic valves along with real-time optical detection, bacteria can be trapped and classified according to their physical shape and size for pathogen classification. By monitoring their growth in the presence of antibiotics at the single-cell level, antimicrobial susceptibility of the bacteria can be determined in as little as 30 minutes compared with days required for standard procedures. The microfluidic system is able to detect bacterial pathogens in urine, blood cultures, and whole blood and can analyze polymicrobial samples. We pilot a study of 25 clinical urine samples to demonstrate the clinical applicability of the microfluidic system. The platform demonstrated a sensitivity of 100% and specificity of 83.33% for pathogen classification and achieved 100% concordance for AST.
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48
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Nemr CR, Smith SJ, Liu W, Mepham AH, Mohamadi RM, Labib M, Kelley SO. Nanoparticle-Mediated Capture and Electrochemical Detection of Methicillin-Resistant Staphylococcus aureus. Anal Chem 2019; 91:2847-2853. [PMID: 30676721 DOI: 10.1021/acs.analchem.8b04792] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The spread of antibiotic-resistant bacteria poses a global threat to public health. Conventional bacterial detection and identification methods often require pre-enrichment and/or sample preprocessing and purification steps that can prolong diagnosis by days. Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most widespread antibiotic-resistant bacteria and is the leading cause of hospital-acquired infections. Here, we have developed a method to specifically capture and detect MRSA directly from patient nasal swabs with no prior culture and minimal processing steps using a microfluidic device and antibody-functionalized magnetic nanoparticles. Bacteria are captured based on antibody recognition of a membrane-bound protein marker that confers β-lactam antibiotic resistance. MRSA identification is then achieved by the use of a strain-specific antibody functionalized with alkaline phosphatase for electrochemical detection. This approach ensures that only those bacteria of the target strain and resistance profile are measured. The method has a limit of detection of 845 CFU/mL and excellent discrimination against high concentrations of common nontarget nasal flora with a turnaround time of under 4.5 h. This detection method was successfully validated using clinical nasal swab specimens ( n = 30) and has the potential to be tailored to various bacterial targets.
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49
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Surrette C, Scherer B, Corwin A, Grossmann G, Kaushik AM, Hsieh K, Zhang P, Liao JC, Wong PK, Wang TH, Puleo CM. Rapid Microbiology Screening in Pharmaceutical Workflows. SLAS Technol 2019; 23:387-394. [PMID: 30027813 DOI: 10.1177/2472630318779758] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recently advances in miniaturization and automation have been utilized to rapidly decrease the time to result for microbiology testing in the clinic. These advances have been made due to the limitations of conventional culture-based microbiology methods, including agar plate and microbroth dilution, which have long turnaround times and require physicians to treat patients empirically with antibiotics before test results are available. Currently, there exist similar limitations in pharmaceutical sterility and bioburden testing, where the long turnaround times associated with standard microbiology testing drive costly inefficiencies in workflows. These include the time lag associated with sterility screening within drug production lines and the warehousing cost and time delays within supply chains during product testing. Herein, we demonstrate a proof-of-concept combination of a rapid microfluidic assay and an efficient cell filtration process that enables a path toward integrating rapid tests directly into pharmaceutical microbiological screening workflows. We demonstrate separation and detection of Escherichia coli directly captured and analyzed from a mammalian (i.e., CHO) cell culture with a 3.0 h incubation. The demonstration is performed using a membrane filtration module that is compatible with sampling from bioreactors, enabling in-line sampling and process monitoring.
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Affiliation(s)
- C Surrette
- 1 Electronics Organization, GE Global Research Center, Niskayuna, NY, USA
| | - B Scherer
- 1 Electronics Organization, GE Global Research Center, Niskayuna, NY, USA
| | - A Corwin
- 1 Electronics Organization, GE Global Research Center, Niskayuna, NY, USA
| | - G Grossmann
- 2 Biology and Physics, GE Global Research Center, Niskayuna, NY, USA
| | - A M Kaushik
- 3 Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - K Hsieh
- 3 Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - P Zhang
- 3 Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - J C Liao
- 4 Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - P K Wong
- 5 Department of Biomedical Engineering, Pennsylvania State University, University Park, PA, USA
| | - T H Wang
- 3 Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - C M Puleo
- 1 Electronics Organization, GE Global Research Center, Niskayuna, NY, USA
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50
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Cross AR, Baldwin VM, Roy S, Essex-Lopresti AE, Prior JL, Harmer NJ. Zoonoses under our noses. Microbes Infect 2019; 21:10-19. [PMID: 29913297 PMCID: PMC6386771 DOI: 10.1016/j.micinf.2018.06.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 11/22/2022]
Abstract
One Health is an effective approach for the management of zoonotic disease in humans, animals and environments. Examples of the management of bacterial zoonoses in Europe and across the globe demonstrate that One Health approaches of international surveillance, information-sharing and appropriate intervention methods are required to successfully prevent and control disease outbreaks in both endemic and non-endemic regions. Additionally, a One Health approach enables effective preparation and response to bioterrorism threats.
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Affiliation(s)
- Alice R Cross
- Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD United Kingdom.
| | - Victoria M Baldwin
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ United Kingdom
| | - Sumita Roy
- Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD United Kingdom
| | | | - Joann L Prior
- Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD United Kingdom; Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ United Kingdom; London School of Hygiene & Tropical Medicine, Kepple Street, London WC1E 7HT United Kingdom
| | - Nicholas J Harmer
- Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD United Kingdom
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