1
|
Zhuang L, Gong J, Zhao Y, Yang J, Liu G, Zhao B, Song C, Zhang Y, Shen Q. Progress in methods for the detection of viable Escherichia coli. Analyst 2024; 149:1022-1049. [PMID: 38273740 DOI: 10.1039/d3an01750h] [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: 01/27/2024]
Abstract
Escherichia coli (E. coli) is a prevalent enteric bacterium and a necessary organism to monitor for food safety and environmental purposes. Developing efficient and specific methods is critical for detecting and monitoring viable E. coli due to its high prevalence. Conventional culture methods are often laborious and time-consuming, and they offer limited capability in detecting potentially harmful viable but non-culturable E. coli in the tested sample, which highlights the need for improved approaches. Hence, there is a growing demand for accurate and sensitive methods to determine the presence of viable E. coli. This paper scrutinizes various methods for detecting viable E. coli, including culture-based methods, molecular methods that target DNAs and RNAs, bacteriophage-based methods, biosensors, and other emerging technologies. The review serves as a guide for researchers seeking additional methodological options and aiding in the development of rapid and precise assays. Moving forward, it is anticipated that methods for detecting E. coli will become more stable and robust, ultimately contributing significantly to the improvement of food safety and public health.
Collapse
Affiliation(s)
- Linlin Zhuang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 211102, P. R. China.
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, P. R. China
| | - Ying Zhao
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 211102, P. R. China.
| | - Jianbo Yang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Guofang Liu
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Bin Zhao
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Chunlei Song
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Yu Zhang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 211102, P. R. China.
| | - Qiuping Shen
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| |
Collapse
|
2
|
Mainelis G. Bioaerosol Sampling: Classical Approaches, Advances, and Perspectives. AEROSOL SCIENCE AND TECHNOLOGY : THE JOURNAL OF THE AMERICAN ASSOCIATION FOR AEROSOL RESEARCH 2020; 54:496-519. [PMID: 35923417 PMCID: PMC9344602 DOI: 10.1080/02786826.2019.1671950] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Bioaerosol sampling is an essential and integral part of any bioaerosol investigation. Since bioaerosols are very diverse in terms of their sizes, species, biological properties, and requirements for their detection and quantification, bioaerosol sampling is an active, yet challenging research area. This paper was inspired by the discussions during the 2018 International Aerosol Conference (IAC) (St. Louis, MO) regarding the need to summarize the current state of the art in bioaerosol research, including bioaerosol sampling, and the need to develop a more standardized set of guidelines for protocols used in bioaerosol research. The manuscript is a combination of literature review and perspectives: it discusses the main bioaerosol sampling techniques and then overviews the latest technical developments in each area; the overview is followed by the discussion of the emerging trends and developments in the field, including personal sampling, application of passive samplers, and advances toward improving bioaerosol detection limits as well as the emerging challenges such as collection of viruses and collection of unbiased samples for bioaerosol sequencing. The paper also discusses some of the practical aspects of bioaerosol sampling with particular focus on sampling aspects that could lead to bioaerosol determination bias. The manuscript concludes by suggesting several goals for bioaerosol sampling and development community to work towards and describes some of the grand bioaerosol challenges discussed at the IAC 2018.
Collapse
Affiliation(s)
- Gediminas Mainelis
- Department of Environmental Sciences, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ 08901, USA
| |
Collapse
|
3
|
Machado-Moreira B, Monteiro S, Santos R, Martinez-Murcia A, Rajkovic A, Smigic N, Richards KG, Abram F, Burgess CM. Impact of beef extract used for sample concentration on the detection of Escherichia coli DNA in water samples via qPCR. J Microbiol Methods 2019; 168:105786. [PMID: 31770538 DOI: 10.1016/j.mimet.2019.105786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 11/26/2022]
Abstract
There is increasing interest in methodologies for the simultaneous concentration and detection of multiple targets in individual samples. The aim of this study was to investigate the potential presence of E. coli DNA in beef extract powder used as part of a procedure to concentrate water samples for the simultaneous detection of bacteria, viruses and protozoa. DNA from E. coli was detected in five out of six beef extract lots tested, demonstrating the limitations of its inclusion when being used in assays that will be used for the detection of E. coli in water samples. Further work is required to clarify if this phenomenon also occurs for other microorganisms of interest in water.
Collapse
Affiliation(s)
- Bernardino Machado-Moreira
- Teagasc Food Research Centre, Ashtown, Dublin, Ireland; Functional Environmental Microbiology, National University of Ireland Galway, Galway, Ireland
| | - Silvia Monteiro
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Ricardo Santos
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | | | - Andreja Rajkovic
- Department of Food Safety and Food Quality Management, University of Belgrade-Faculty of Agriculture, Serbia; Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University; Belgium
| | - Nada Smigic
- Department of Food Safety and Food Quality Management, University of Belgrade-Faculty of Agriculture, Serbia
| | - Karl G Richards
- Teagasc Johnstown Castle Environmental Research Centre, Wexford, Ireland
| | - Florence Abram
- Functional Environmental Microbiology, National University of Ireland Galway, Galway, Ireland
| | | |
Collapse
|
4
|
Kearns EA, Gustafson RE, Castillo SM, Alnughaymishi H, Lim DV, Ryser ET. Rapid large-volume concentration for increased detection of Escherichia coli O157:H7 and Listeria monocytogenes in lettuce wash water generated at commercial facilities. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
5
|
Chylewska A, Ogryzek M, Makowski M. Modern Approach to Medical Diagnostics - the Use of Separation Techniques in Microorganisms Detection. Curr Med Chem 2019; 26:121-165. [DOI: 10.2174/0929867324666171023164813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 04/20/2017] [Accepted: 05/20/2016] [Indexed: 11/22/2022]
Abstract
Background:Analytical chemistry and biotechnology as an interdisciplinary fields of science have been developed during many years and are experiencing significant growth, to cover a wide range of microorganisms separation techniques and methods, utilized for medical therapeutic and diagnostic purposes. Currently scientific reports contribute by introducing electrophoretical and immunological methods and formation of devices applied in food protection (avoiding epidemiological diseases) and healthcare (safety ensuring in hospitals).Methods:Electrophoretic as well as nucleic-acid-based or specific immunological methods have contributed tremendously to the advance of analyses in recent three decades, particularly in relation to bacteria, viruses and fungi identifications, especially in medical in vitro diagnostics, as well as in environmental or food protection.Results:The paper presents the pathogen detection competitiveness of these methods against conventional ones, which are still too time consuming and also labor intensive. The review is presented in several parts following the current trends in improved pathogens separation and detection methods and their subsequent use in medical diagnosis.Discussion:Part one, consists of elemental knowledge about microorganisms as an introduction to their characterization: descriptions of divisions, sizes, membranes (cells) components. Second section includes the development, new technological and practical solution descriptions used in electrophoretical procedures during microbes analyses, with special attention paid to bio-samples analyses like blood, urine, lymph or wastewater. Third part covers biomolecular areas that have created a basis needed to identify the progress, limitations and challenges of nucleic-acid-based and immunological techniques discussed to emphasize the advantages of new separative techniques in selective fractionating of microorganisms.
Collapse
Affiliation(s)
- Agnieszka Chylewska
- Laboratory of Intermolecular Interactions, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80- 308 Gdansk, Poland
| | - Małgorzata Ogryzek
- Laboratory of Intermolecular Interactions, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80- 308 Gdansk, Poland
| | - Mariusz Makowski
- Laboratory of Intermolecular Interactions, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80- 308 Gdansk, Poland
| |
Collapse
|
6
|
Ximenes E, Ku S, Hoagland L, Ladisch MR. Accelerated Sample Preparation for Fast Salmonella Detection in Poultry Products. Methods Mol Biol 2019; 1918:3-20. [PMID: 30580395 DOI: 10.1007/978-1-4939-9000-9_1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Salmonella is the most burdensome foodborne pathogen in the USA and a major causal agent of foodborne outbreaks. Detection of a pathogen such as Salmonella can be achieved within a few hours using commercially available rapid methods, but the sample preparation is time consuming and may require multiple days. We have developed and successfully tested an accelerated sample preparation method based on microfiltration, in some cases preceded by a short enrichment step, for the rapid detection of selected pathogens. The time-frame of the overall process, from sample preparation (i.e., food rinse or homogenate preparation, microbial enrichment, and filtration steps) to detection is 8 h or less. While microfiltration has been practiced for 70 years, the complex interactions between food substances and filter membrane surfaces have shown that food pretreatment methods need to be developed on a case by case basis for the recovery of bacteria from food homogenates and/or rinses. We have also demonstrated that addition of protease to treat homogenates of different poultry products prior to microfiltration avoids the rapid decrease in flux that otherwise occurs during microfiltration. This protease treatment minimizes filter clogging, so that the microbial concentration, recovery and detection of 1 to 10 CFU/g of Salmonella in poultry products is possible in less than 8 h.
Collapse
Affiliation(s)
- Eduardo Ximenes
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, USA
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, IN, USA
| | - Seockmo Ku
- Fermentation Science Program, School of Agribusiness and Agriscience, College of Basic and Applied Sciences, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Lori Hoagland
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, USA
| | - Michael R Ladisch
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, USA.
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, IN, USA.
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
7
|
Lomakina GY, Modestova YA, Ugarova NN. Bioluminescence assay for cell viability. BIOCHEMISTRY (MOSCOW) 2016; 80:701-13. [PMID: 26531016 DOI: 10.1134/s0006297915060061] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Theoretical aspects of the adenosine triphosphate bioluminescence assay based on the use of the firefly luciferin-luciferase system are considered, as well as its application for assessing cell viability in microbiology, sanitation, medicine, and ecology. Various approaches for the analysis of individual or mixed cultures of microorganisms are presented, and capabilities of the method for investigation of biological processes in live cells including necrosis, apoptosis, as well as for investigation of the dynamics of metabolism are described.
Collapse
Affiliation(s)
- G Yu Lomakina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | | | | |
Collapse
|
8
|
Vibbert HB, Ku S, Li X, Liu X, Ximenes E, Kreke T, Ladisch MR, Deering AJ, Gehring AG. Accelerating sample preparation through enzyme-assisted microfiltration ofSalmonellain chicken extract. Biotechnol Prog 2015; 31:1551-62. [PMID: 26400739 DOI: 10.1002/btpr.2167] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/11/2015] [Indexed: 01/31/2023]
Affiliation(s)
- Hunter B. Vibbert
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Chemistry; Purdue University; West Lafayette IN 47907
| | - Seockmo Ku
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Agricultural and Biological Engineering; Purdue University; West Lafayette IN 47907
| | - Xuan Li
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Agricultural and Biological Engineering; Purdue University; West Lafayette IN 47907
| | - Xingya Liu
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Agricultural and Biological Engineering; Purdue University; West Lafayette IN 47907
| | - Eduardo Ximenes
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Agricultural and Biological Engineering; Purdue University; West Lafayette IN 47907
| | - Thomas Kreke
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Agricultural and Biological Engineering; Purdue University; West Lafayette IN 47907
- Weldon School of Biomedical Engineering; Purdue University; West Lafayette IN 47907
| | - Michael R. Ladisch
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Agricultural and Biological Engineering; Purdue University; West Lafayette IN 47907
- Weldon School of Biomedical Engineering; Purdue University; West Lafayette IN 47907
| | | | - Andrew G. Gehring
- US Department of Agriculture; Agricultural Research Service; Wyndmoor PA 19038
| |
Collapse
|
9
|
Highly selective and sensitive electrochemical biosensor for ATP based on the dual strategy integrating the cofactor-dependent enzymatic ligation reaction with self-cleaving DNAzyme-amplified electrochemical detection. Biosens Bioelectron 2014; 63:14-20. [PMID: 25048448 DOI: 10.1016/j.bios.2014.07.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 07/04/2014] [Accepted: 07/04/2014] [Indexed: 11/22/2022]
Abstract
A dual strategy that combines the adenosine triphosphate (ATP)-dependent enzymatic ligation reaction with self-cleaving DNAzyme-amplified electrochemical detection is employed to construct the biosensor. In this design, the methylene blue-labeled hairpin-structured DNA was self-assembled onto a gold electrode surface to prepare the modified electrode through the interaction of Au-S bond. In the procedure of ATP-dependent ligation reaction, when the specific cofactor ATP was added, the two split oligonucleotide fragments of 8-17 DNAzyme were linked by T4 DNA ligase and then released to hybridize with the labeled hairpin-structured DNA substrate. The linked 8-17 DNAzyme catalyzes the cleavage of the hairpin-structured substrate by the addition of Zn(2+), causing the methylene blue which contains high electrochemical activity to leave the surface of the gold electrode, therefore generating a dramatic decrease of electrochemical signal. The decrease of peak current was readily measured by square wave voltammetry and a relatively low detection limit (0.05 nM) was obtained with a linear response range from 0.1 to 1000 nM. By taking advantage of the highly specific cofactor dependence of the DNA ligation reaction, the proposed ligation-induced DNAzyme cascades demonstrate ultrahigh selectivity toward the target cofactor ATP. A catalytic and molecular beacons strategy is further adopted to amplify the electrochemical signal detection achieved by cycling and regenerating the 8-17 DNAzyme to realize enzymatic multiple turnover, thus one DNAzyme can catalyze the cleavage of several hairpin-structured substrates, which improves the sensitivity of the newly designed electrochemical sensing system.
Collapse
|
10
|
An IMS/ATP Assay for the Detection of Mycobacterium tuberculosis in Urine. Tuberc Res Treat 2012; 2012:292605. [PMID: 22655193 PMCID: PMC3357591 DOI: 10.1155/2012/292605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 02/15/2012] [Accepted: 02/18/2012] [Indexed: 11/18/2022] Open
Abstract
Background. Although sputum smears are the gold standard for diagnosis of tuberculosis, sensitivity in HIV/TB coinfection cases is low, indicating a need for alternative methods. Urine is being increasingly evaluated. Materials and Methods. A novel method for detecting Mycobacterium tuberculosis (MTB) in synthetic urine using a combined IMS/ATP assay was evaluated. Preliminary work established standard ATP conditions and the sensitivity and specificity of the MTB antibody. Eighty-four blinded samples in four replicate assays were evaluated for the presence of MTB using labeled immunomagnetic beads for capture. Beads were separated, washed, and resuspended in broth and added to a microtiter plate. Bioluminescent output was measured and signal-to-noise ratios were calculated. All samples were plated on Middlebrook 7H10 agar or trypticase soy agar to determine limit of detection and recoveries. Results and Conclusions. MTB was distinguished from common bacteriuria isolates and other nontarget bacteria by its ATP results. IMS/ATP successfully detected 19 of 28 samples of MTB in synthetic urine with a limit of detection of 104 CFU/ml. Sensitivity and specificity were 67.9% and 82.1%, respectively. This assay offers a possible rapid screening method for HIV-positive patients with suspected coinfection to improve MTB diagnosis.
Collapse
|
11
|
López-Campos G, Martínez-Suárez JV, Aguado-Urda M, López-Alonso V. Detection, Identification, and Analysis of Foodborne Pathogens. SPRINGERBRIEFS IN FOOD, HEALTH, AND NUTRITION 2012. [DOI: 10.1007/978-1-4614-3250-0_2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
|