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Rubens RS, Arruda IDSA, Almeida RM, Nóbrega YKDM, Carneiro MDS, Dalmolin TV. Challenges in the Detection of Polymyxin Resistance: From Today to the Future. Microorganisms 2024; 12:101. [PMID: 38257928 PMCID: PMC10818861 DOI: 10.3390/microorganisms12010101] [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: 10/30/2023] [Revised: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Antimicrobial resistance is known to be one of the greatest global threats to human health, and is one of the main causes of death worldwide. In this scenario, polymyxins are last-resort antibiotics to treat infections caused by multidrug-resistant bacteria. Currently, the reference test to evaluate the susceptibility of isolates to polymyxins is the broth microdilution method; however, this technique has numerous complications and challenges for use in laboratory routines. Several phenotypic methods have been reported as being promising for implementation in routine diagnostics, including the BMD commercial test, rapid polymyxin NP test, polymyxin elution test, culture medium with polymyxins, and the Polymyxin Drop Test, which require materials for use in routines and must be easy to perform. Furthermore, Sensititre®, molecular tests, MALDI-TOF MS, and Raman spectroscopy present reliable results, but the equipment is not found in most microbiology laboratories. In this context, this review discusses the main laboratory methodologies that allow the detection of resistance to polymyxins, elucidating the challenges and perspectives.
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Affiliation(s)
- Rebeca Siqueira Rubens
- Laboratório de Microbiologia e Imunologia Clínica (LabMIC), Departamento de Farmácia, Faculdade de Ciências da Saúde, Universidade de Brasília (UnB), Brasília 70910-900, DF, Brazil; (R.S.R.); (I.d.S.A.A.); (R.M.A.); (Y.K.d.M.N.)
| | - Isabel de Souza Andrade Arruda
- Laboratório de Microbiologia e Imunologia Clínica (LabMIC), Departamento de Farmácia, Faculdade de Ciências da Saúde, Universidade de Brasília (UnB), Brasília 70910-900, DF, Brazil; (R.S.R.); (I.d.S.A.A.); (R.M.A.); (Y.K.d.M.N.)
| | - Rosane Mansan Almeida
- Laboratório de Microbiologia e Imunologia Clínica (LabMIC), Departamento de Farmácia, Faculdade de Ciências da Saúde, Universidade de Brasília (UnB), Brasília 70910-900, DF, Brazil; (R.S.R.); (I.d.S.A.A.); (R.M.A.); (Y.K.d.M.N.)
| | - Yanna Karla de Medeiros Nóbrega
- Laboratório de Microbiologia e Imunologia Clínica (LabMIC), Departamento de Farmácia, Faculdade de Ciências da Saúde, Universidade de Brasília (UnB), Brasília 70910-900, DF, Brazil; (R.S.R.); (I.d.S.A.A.); (R.M.A.); (Y.K.d.M.N.)
| | | | - Tanise Vendruscolo Dalmolin
- Laboratório de Microbiologia e Imunologia Clínica (LabMIC), Departamento de Farmácia, Faculdade de Ciências da Saúde, Universidade de Brasília (UnB), Brasília 70910-900, DF, Brazil; (R.S.R.); (I.d.S.A.A.); (R.M.A.); (Y.K.d.M.N.)
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Liao X, Deng R, Warriner K, Ding T. Antibiotic resistance mechanism and diagnosis of common foodborne pathogens based on genotypic and phenotypic biomarkers. Compr Rev Food Sci Food Saf 2023; 22:3212-3253. [PMID: 37222539 DOI: 10.1111/1541-4337.13181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/22/2023] [Accepted: 05/06/2023] [Indexed: 05/25/2023]
Abstract
The emergence of antibiotic-resistant bacteria due to the overuse or inappropriate use of antibiotics has become a significant public health concern. The agri-food chain, which serves as a vital link between the environment, food, and human, contributes to the large-scale dissemination of antibiotic resistance, posing a concern to both food safety and human health. Identification and evaluation of antibiotic resistance of foodborne bacteria is a crucial priority to avoid antibiotic abuse and ensure food safety. However, the conventional approach for detecting antibiotic resistance heavily relies on culture-based methods, which are laborious and time-consuming. Therefore, there is an urgent need to develop accurate and rapid tools for diagnosing antibiotic resistance in foodborne pathogens. This review aims to provide an overview of the mechanisms of antibiotic resistance at both phenotypic and genetic levels, with a focus on identifying potential biomarkers for diagnosing antibiotic resistance in foodborne pathogens. Furthermore, an overview of advances in the strategies based on the potential biomarkers (antibiotic resistance genes, antibiotic resistance-associated mutations, antibiotic resistance phenotypes) for antibiotic resistance analysis of foodborne pathogens is systematically exhibited. This work aims to provide guidance for the advancement of efficient and accurate diagnostic techniques for antibiotic resistance analysis in the food industry.
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Affiliation(s)
- Xinyu Liao
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- School of Mechanical and Energy Engineering, NingboTech University, Ningbo, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu, Sichuan, China
| | - Keith Warriner
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | - Tian Ding
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou, Zhejiang, China
- Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, Zhejiang, China
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Srivastava P, Prasad D. Isothermal nucleic acid amplification and its uses in modern diagnostic technologies. 3 Biotech 2023; 13:200. [PMID: 37215369 PMCID: PMC10193355 DOI: 10.1007/s13205-023-03628-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Nucleic acids are prominent biomarkers for diagnosing infectious pathogens using nucleic acid amplification techniques (NAATs). PCR, a gold standard technique for amplifying nucleic acids, is widely used in scientific research and diagnosis. Efficient pathogen detection is a key to adequate food safety and hygiene. However, using bulky thermal cyclers and costly laboratory setup limits its uses in developing countries, including India. The isothermal amplification methods are exploited to develop miniaturized sensors against viruses, bacteria, fungi and other pathogenic organisms and have been applied for in situ diagnosis. Isothermal amplification techniques have been found suitable for POC techniques and follow WHO's ASSURED criteria. LAMP, NASBA, SDA, RCA and RPA are some of the isothermal amplification techniques which are preferable for POC diagnostics. Furthermore, methods such as WGA, CPA, HDA, EXPAR, SMART, SPIA and DAMP were introduced for even more accuracy and robustness. Using recombinant polymerases and other nucleic acid-modifying enzymes has dramatically broadened the detection range of target pathogens under the scanner. The coupling of isothermal amplification methods with advanced technologies such as CRISPR/Cas systems, fluorescence-based chemistries, microfluidics and paper-based sensors has significantly influenced the biosensing and diagnosis field. This review comprehensively analyzed isothermal nucleic acid amplification methods, emphasizing their advantages, disadvantages and limitations.
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Affiliation(s)
- Pulkit Srivastava
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
| | - Dinesh Prasad
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
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Tao J, Liu D, Xiong J, Dou L, Zhai W, Zhang R, Wang Y, Shen J, Wen K. Rapid On-Site Detection of Extensively Drug-Resistant Genes in Enterobacteriaceae via Enhanced Recombinase Polymerase Amplification and Lateral Flow Biosensor. Microbiol Spectr 2022; 10:e0334422. [PMID: 36445091 PMCID: PMC9769758 DOI: 10.1128/spectrum.03344-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/14/2022] [Indexed: 12/03/2022] Open
Abstract
The widespread emergence of transferable extensively drug-resistant (XDR) genes, including blaNDM and blaKPC for carbapenem resistance, mcr-1 for colistin resistance, and tet(X4) and tet(X6) for tigecycline resistance, in Enterobacteriaceae poses a major threat to public health. Thus, rapid on-site detection of these XDR genes is urgently needed. We developed a cascade system with a unitary polyethylene glycol (PEG) 200-enhanced recombinase polymerase amplification (RPA) as the core, combined with a modified Chelex-100 lysis method and a horseradish peroxidase (HRP)-catalyzed lateral flow immunoassay (LFIA) biosensor, to accurately detect these genes in Enterobacteriaceae. The conventional Chelex-100 lysis method was modified to allow in situ extraction of bacterial DNA in 20 min without requiring bulky high-speed centrifuges. Using PEG 200 increased the amplification efficiency of the RPA by 13%, and the HRP-catalyzed LFIA biosensor intensified the colorimetric signal of the test line. Following optimization, the sensitivity of the cascade system was <10 copies/μL with satisfactory specificity, allowing for highly sensitive detection of these XDR genes in Enterobacteriaceae. The complete detection procedure can be completed in less than 1 h without using large-scale instruments. This assay is conducive to rapid on-site visual detection of these XDR genes in Enterobacteriaceae in practical applications, thus providing better technical support for clinical surveillance of these genes and better treatment of XDR pathogens. IMPORTANCE Carbapenem, colistin, and tigecycline are considered the last resorts for treating severe bacterial infections caused by extensively drug-resistant (XDR) pathogens. A major threat to public health is the emergence and prevalence of transferable XDR genes in Enterobacteriaceae, such as blaNDM and blaKPC for carbapenem resistance, mcr-1 for colistin resistance, and tet(X4) and tet(X6) for tigecycline resistance. Therefore, it is imperative to develop rapid on-site methods to detect these XDR genes. In this study, we constructed a cascade system for detecting these genes based on PEG 200-enhanced recombinase polymerase amplification combined with a modified Chelex-100 lysis method and HRP-catalyzed lateral flow immunoassay. The current method is capable of detecting the above-mentioned XDR genes in situ with satisfactory specificity and sensitivity, which could provide technical support for the surveillance of these genes and provide medication recommendations for the treatment of relevant clinical infections.
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Affiliation(s)
- Jin Tao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Dejun Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jincheng Xiong
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Leina Dou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Weishuai Zhai
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Rong Zhang
- Clinical Microbiology Laboratory, 2nd Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
| | - Kai Wen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, People’s Republic of China
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Gong L, Jin Z, Liu E, Tang F, Yuan F, Liang J, Wang Y, Liu X, Wang Y. Highly Sensitive and Specific Detection of Mobilized Colistin Resistance Gene mcr-1 by CRISPR-Based Platform. Microbiol Spectr 2022; 10:e0188422. [PMID: 36043860 PMCID: PMC9602551 DOI: 10.1128/spectrum.01884-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/15/2022] [Indexed: 12/31/2022] Open
Abstract
Mobilized colistin resistance (mcr-1) gene mediated by plasmid can cause the speediness dissemination of colistin-resistant strains, which have given rise to a great threat to the treatment of human infection. Hence, a rapid and accurate diagnosis technology for detecting mcr-1 is essential for the control of resistance gene. Here, a recombinase polymerase amplification (RPA) coupled with CRISPR/Cas12a platform was established for rapid, sensitive, and specific detection of mcr-1 gene. The analytical sensitivity of our assay is 420 fg per reaction in pure mcr-1-positive isolates, and the threshold of this method in spiked clinical samples was down to 1.6 × 103 ~ 6.2 × 103 CFU/mL (1.6 ~ 6.2 CFU/reaction). Moreover, the RPA-CRISPR/Cas12a system perspicuously demonstrated no cross-reactivity with other resistant genes. The entire experimental process included rapid DNA extraction (15 min), RPA reaction (30 min), CRISPR/Cas12a cleavage (5 min), and fluorescence testing (<10 min), which could be completed within 60 min. In summary, the RPA-CRISPR/Cas12a assay designed here provides a rapid diagnostic way for monitoring mcr-1 in clinic and livestock farm. IMPORTANCE This study promises a rapid and accurate assay (RPA-CRISPR/Cas12a) for the surveillance of mcr-1 gene, which causes the efficacy loss of colistin in clinical treatments. In addition, the established method is fit for "on-site" surveillance especially.
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Affiliation(s)
- Lin Gong
- Department of Disinfection and Pest Control, Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Zhengjiang Jin
- Department of Clinical Laboratory, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Ernan Liu
- Department of Disinfection and Pest Control, Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Fei Tang
- Institute of Environmental Medicine, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fengyun Yuan
- Institute of Environmental Medicine, MOE Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiansheng Liang
- Department of Disinfection and Pest Control, Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Yimei Wang
- Department of Disinfection and Pest Control, Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Xiaoli Liu
- Department of Disinfection and Pest Control, Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Yi Wang
- Experimental Research Center, Capital Institute of Pediatrics, Beijing, China
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Boutal H, Moguet C, Pommiès L, Simon S, Naas T, Volland H. The Revolution of Lateral Flow Assay in the Field of AMR Detection. Diagnostics (Basel) 2022; 12:1744. [PMID: 35885647 PMCID: PMC9317642 DOI: 10.3390/diagnostics12071744] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
The global spread of antimicrobial resistant (AMR) bacteria represents a considerable public health concern, yet their detection and identification of their resistance mechanisms remain challenging. Optimal diagnostic tests should provide rapid results at low cost to enable implementation in any microbiology laboratory. Lateral flow assays (LFA) meet these requirements and have become essential tools to combat AMR. This review presents the versatility of LFA developed for the AMR detection field, with particular attention to those directly triggering β-lactamases, their performances, and specific limitations. It considers how LFA can be modified by detecting not only the enzyme, but also its β-lactamase activity for a broader clinical sensitivity. Moreover, although LFA allow a short time-to-result, they are generally only implemented after fastidious and time-consuming techniques. We present a sample processing device that shortens and simplifies the handling of clinical samples before the use of LFA. Finally, the capacity of LFA to detect amplified genetic determinants of AMR by isothermal PCR will be discussed. LFA are inexpensive, rapid, and efficient tools that are easy to implement in the routine workflow of laboratories as new first-line tests against AMR with bacterial colonies, and in the near future directly with biological media.
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Affiliation(s)
- Hervé Boutal
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
| | - Christian Moguet
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
| | - Lilas Pommiès
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
| | - Stéphanie Simon
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
| | - Thierry Naas
- Bacteriology-Hygiene Unit, APHP, Hôpital Bicêtre, 94270 Le Kremlin-Bicêtre, France;
- Team Resist, UMR1184, Université Paris-Saclay—INSERM—CEA, LabEx Lermit, 91190 Gif-sur-Yvette, France
- Associated French National Reference Center for Antibiotic Resistance: Carbapenemase-Producing Enterobacteriaceae, 94270 Le Kremlin-Bicêtre, France
| | - Hervé Volland
- Département Médicaments et Technologies Pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 91191 Gif-sur-Yvette, France; (H.B.); (C.M.); (L.P.); (S.S.)
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Smelikova E, Tkadlec J, Krutova M. How to: screening for mcr-mediated resistance to colistin. Clin Microbiol Infect 2021; 28:43-50. [PMID: 34537365 DOI: 10.1016/j.cmi.2021.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND Colistin belongs to the last-resort antibiotics. The discovery of plasmid-bound colistin resistance mediated by the mcr-gene(s) is of great concern because, given its biological potential, there is a risk of its rapid spread. OBJECTIVES To discuss the current literature on the methods for the screening for mcr-mediated resistance to colistin. SOURCES Literature was drawn from a search of PubMed from 1 January 2016 to 26 April 2021. CONTENT The selective culture-based or culture-independent approach can be used for the screening of mcr-mediated resistance to colistin in clinical samples. Rapid Polymyxin NP, Colistin Drop or Colistin Agar Spot tests are applicable for the selection of isolates with a suspected resistance to colistin that has to be confirmed by broth microdilution. The mcr-mediated resistance to colistin can be confirmed by the detection of the causal gene(s) or by phenotype using EDTA-colistin broth disc elution; production of the MCR-1 enzyme can be confirmed with lateral flow immunoassay, using matrix-assisted laser desorption/ionization time-of flight or liquid chromatography-based mass spectrometry. Whole-genome sequencing (WGS) is the ultimate typing method. When a WGS platform is not available at a healthcare facility, a WGS-outsourced service, in combination with freely available bioinformatics tools, allows for the characterization of the mcr-gene(s) carrying isolates. IMPLICATIONS mcr-mediated colistin resistance should be monitored through active targeted screening. The broth microdilution method is required for colistin susceptibility testing but as only a selected number of clinical isolates are tested, colistin resistance, including mcr-mediated, may remain undetected. In mcr-1-positive Escherichia coli isolates, the MIC to colistin can range from 2 to 8 mg/L, so it is proposed that Enterobacterales with a colistin MIC of 2 mg/L should also be included in the mcr-mediated colistin resistance screening and those with a confirmed mcr-genotype and/or MCR-phenotype should be considered to be colistin-resistant.
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Affiliation(s)
- Eva Smelikova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Czech Republic
| | - Jan Tkadlec
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Czech Republic
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Czech Republic.
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