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Sousa JM, Barbosa A, Araújo D, Castro J, Azevedo NF, Cerqueira L, Almeida C. Evaluation of Simultaneous Growth of Escherichia coli O157:H7, Salmonella spp., and Listeria monocytogenes in Ground Beef Samples in Different Growth Media. Foods 2024; 13:2095. [PMID: 38998601 PMCID: PMC11240903 DOI: 10.3390/foods13132095] [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: 05/28/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Several multiplex approaches for the simultaneous detection of pathogens in food have been developed in recent years, but the use of a single enrichment medium remains a problem. In this study, six enrichment broths (five non-selective media, tryptic soy broth (TSB), brain heart infusion broth (BHI), buffered peptone water (BPW), universal pre-enrichment broth (UPB), no. 17 broth, and a selective, Salmonella Escherichia Listeria broth (SEL)), were studied for the simultaneous detection of E. coli O157:H7, Salmonella spp., and L. monocytogenes, to validate the suitable enrichment broth to be used for the detection methods. Different ratios of E. coli O157:H7, Salmonella spp., and L. monocytogenes were used. Almost all non-selective broths evaluated in this study showed similar growth parameters and profiles among each other. The only selective enrichment broth under analysis (SEL) showed distinct growth features compared to the non-selective media, allowing for a slower but balanced growth of the three pathogens, which could be beneficial in preventing the overgrowth of fast-growing bacteria. In addition, when tested in ground beef samples, SEL broth seems to be the most distinctive medium with a balanced growth pattern observed for the three pathogens. Overall, this study is intended to provide the basis for the selection of suitable enrichment broths according to the technology detection to be used, the desired time of enrichment, and the expected balanced concentration of pathogens.
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Affiliation(s)
- José Mário Sousa
- CEB-Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
| | - Ana Barbosa
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Daniela Araújo
- CEB-Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, 4485-655 Vila do Conde, Portugal
- LABBELS-Associate Laboratory, 4710-057 Braga, Portugal
| | - Joana Castro
- CEB-Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, 4485-655 Vila do Conde, Portugal
| | - Nuno Filipe Azevedo
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Laura Cerqueira
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Carina Almeida
- CEB-Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- ALiCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, 4485-655 Vila do Conde, Portugal
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2
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Kim D, Kim M. Sensitive detection of viable Cronobacter sakazakii by bioluminescent reporter phage emitting stable signals with truncated holin. Food Res Int 2023; 174:113665. [PMID: 37981373 DOI: 10.1016/j.foodres.2023.113665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/21/2023]
Abstract
As outbreaks of foodborne illness caused by the opportunistic pathogen Cronobacter sakazakii (Cs) continue to occur, particularly in infants consuming powdered infant formula (PIF), the need for sensitive, rapid, and easy-to-use detection of Cs from food and food processing environments is increasing. Here, we developed bioluminescent reporter bacteriophages for viable Cs-specific, substrate-free, rapid detection by introducing luciferase and its corresponding substrate-providing enzyme complex into the virulent phage ΦC01. Although the reporter phage ΦC01_lux, constructed by replacing non-essential genes for phage infectivity with a luxCDABE reporter operon, produced bioluminescence upon Cs infection, the emitted signal was quickly decayed due to the superior bacteriolytic activity of ΦC01. By truncating the membrane pore-forming protein holin and thus limiting its function, the bacterial lysis was delayed and the resultant engineered reporter phage ΦC01_lux_Δhol could produce a more stable and reliable bioluminescent signal. Accordingly, ΦC01_lux_Δhol was able to detect at least an average of 2 CFU/ml of Cs artificially contaminated PIF and Sunsik and food contact surface models within a total of 7 h of assays, including 5 h of pre-enrichment for Cs amplification. The sensitive, easy-to-use, and specific detection of live Cs with the developed reporter phage could be applied as a novel complementary tool for monitoring Cs in food and food-related environments for food safety and public health.
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Affiliation(s)
- Doyeon Kim
- Laboratory of Molecular Food Microbiology, Department of Food and Nutrition, Brain Korea 21 FOUR, College of Human Ecology, Yonsei University, Seoul 03722, Republic of Korea
| | - Minsik Kim
- Laboratory of Molecular Food Microbiology, Department of Food and Nutrition, Brain Korea 21 FOUR, College of Human Ecology, Yonsei University, Seoul 03722, Republic of Korea.
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3
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Mousavi ZE, Hunt K, Koolman L, Butler F, Fanning S. Cronobacter Species in the Built Food Production Environment: A Review on Persistence, Pathogenicity, Regulation and Detection Methods. Microorganisms 2023; 11:1379. [PMID: 37374881 DOI: 10.3390/microorganisms11061379] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
The powdered formula market is large and growing, with sales and manufacturing increasing by 120% between 2012 and 2021. With this growing market, there must come an increasing emphasis on maintaining a high standard of hygiene to ensure a safe product. In particular, Cronobacter species pose a risk to public health through their potential to cause severe illness in susceptible infants who consume contaminated powdered infant formula (PIF). Assessment of this risk is dependent on determining prevalence in PIF-producing factories, which can be challenging to measure with the heterogeneity observed in the design of built process facilities. There is also a potential risk of bacterial growth occurring during rehydration, given the observed persistence of Cronobacter in desiccated conditions. In addition, novel detection methods are emerging to effectively track and monitor Cronobacter species across the food chain. This review will explore the different vehicles that lead to Cronobacter species' environmental persistence in the food production environment, as well as their pathogenicity, detection methods and the regulatory framework surrounding PIF manufacturing that ensures a safe product for the global consumer.
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Affiliation(s)
- Zeinab Ebrahimzadeh Mousavi
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland
- School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8 Dublin, Ireland
- Department of Food Science and Engineering, Faculties of Agriculture and Natural Resources, University of Tehran, Karaj 6719418314, Iran
| | - Kevin Hunt
- School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8 Dublin, Ireland
| | - Leonard Koolman
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland
| | - Francis Butler
- School of Biosystems and Food Engineering, University College Dublin, Belfield, Dublin 4, D04 V1W8 Dublin, Ireland
| | - Séamus Fanning
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, D04 V1W8 Dublin, Ireland
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4
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Nácher-Vázquez M, Barbosa A, Armelim I, Azevedo AS, Almeida GN, Pizarro C, Azevedo NF, Almeida C, Cerqueira L. Development of a Novel Peptide Nucleic Acid Probe for the Detection of Legionella spp. in Water Samples. Microorganisms 2022; 10:1409. [PMID: 35889127 PMCID: PMC9318766 DOI: 10.3390/microorganisms10071409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023] Open
Abstract
Legionella are opportunistic intracellular pathogens that are found throughout the environment. The Legionella contamination of water systems represents a serious social problem that can lead to severe diseases, which can manifest as both Pontiac fever and Legionnaires' disease (LD) infections. Fluorescence in situ hybridization using nucleic acid mimic probes (NAM-FISH) is a powerful and versatile technique for bacterial detection. By optimizing a peptide nucleic acid (PNA) sequence based on fluorescently selective binding to specific bacterial rRNA sequences, we established a new PNA-FISH method that has been successfully designed for the specific detection of the genus Legionella. The LEG22 PNA probe has shown great theoretical performance, presenting 99.9% specificity and 96.9% sensitivity. We also demonstrated that the PNA-FISH approach presents a good signal-to-noise ratio when applied in artificially contaminated water samples directly on filtration membranes or after cells elution. For water samples with higher turbidity (from cooling tower water systems), there is still the need for further method optimization in order to detect cellular contents and to overcome interferents' autofluorescence, which hinders probe signal visualization. Nevertheless, this work shows that the PNA-FISH approach could be a promising alternative for the rapid (3-4 h) and accurate detection of Legionella.
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Affiliation(s)
- Montserrat Nácher-Vázquez
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- INIAV, IP—National Institute for Agrarian and Veterinary Research, Vairão, 4485-655 Vila Do Conde, Portugal;
| | - Ana Barbosa
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Inês Armelim
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
| | - Andreia Sofia Azevedo
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP—Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Gonçalo Nieto Almeida
- INIAV, IP—National Institute for Agrarian and Veterinary Research, Vairão, 4485-655 Vila Do Conde, Portugal;
| | - Cristina Pizarro
- INSA—National Institute of Health Doutor Ricardo Jorge, Rua Alexandre Herculano 321, 4000-055 Porto, Portugal;
| | - Nuno Filipe Azevedo
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Carina Almeida
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- INIAV, IP—National Institute for Agrarian and Veterinary Research, Vairão, 4485-655 Vila Do Conde, Portugal;
- Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Laura Cerqueira
- LEPABE—Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; (M.N.-V.); (A.B.); (I.A.); (A.S.A.); (N.F.A.); (C.A.)
- ALiCE—Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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5
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The role of Nucleic Acid Mimics (NAMs) on FISH-based techniques and applications for microbial detection. Microbiol Res 2022; 262:127086. [PMID: 35700584 DOI: 10.1016/j.micres.2022.127086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 01/07/2023]
Abstract
Fluorescent in situ hybridization (FISH) is a powerful tool that for more than 30 years has allowed to detect and quantify microorganisms as well as to study their spatial distribution in three-dimensional structured environments such as biofilms. Throughout these years, FISH has been improved in order to face some of its earlier limitations and to adapt to new research objectives. One of these improvements is related to the emergence of Nucleic Acid Mimics (NAMs), which are now employed as alternatives to the DNA and RNA probes that have been classically used in FISH. NAMs such as peptide and locked nucleic acids (PNA and LNA) have provided enhanced sensitivity and specificity to the FISH technique, as well as higher flexibility in terms of applications. In this review, we aim to cover the state-of-the-art of the different NAMs and explore their possible applications in FISH, providing a general overview of the technique advancement in the last decades.
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6
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Oliveira R, Almeida C, Azevedo NF. Detection of Microorganisms by Fluorescence In Situ Hybridization Using Peptide Nucleic Acid. Methods Mol Biol 2021; 2105:217-230. [PMID: 32088873 DOI: 10.1007/978-1-0716-0243-0_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Fluorescence in situ hybridization (FISH) is a 30-year-old technology that has evolved continuously and is now one of the most well-established molecular biology techniques. Traditionally, DNA probes are used for in situ hybridization. However, synthetic molecules are emerging as very promising alternatives, providing better hybridization performance and making FISH procedures easier and more efficient. In this chapter, we describe a universal FISH protocol, using nucleic acid probes, for the detection of bacteria. This protocol should be easily applied to different microorganisms as a way of identifying in situ relevant microorganisms (including pathogens) and their distribution patterns in different types of samples.
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Affiliation(s)
- Ricardo Oliveira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Vairao, Portugal
| | - Carina Almeida
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Vairao, Portugal.,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal.
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7
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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: 140] [Impact Index Per Article: 35.0] [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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8
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Akineden Ö, Wittwer T, Geister K, Plötz M, Usleber E. Nucleic acid lateral flow immunoassay (NALFIA) with integrated DNA probe degradation for the rapid detection of Cronobacter sakazakii and Cronobacter malonaticus in powdered infant formula. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106952] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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9
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Araújo D, Azevedo NM, Barbosa A, Almeida C, Rodrigues ME, Henriques M, Silva S. Application of 2'-OMethylRNA' Antisense Oligomer to Control Candida albicans EFG1 Virulence Determinant. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 18:508-517. [PMID: 31671344 PMCID: PMC6838528 DOI: 10.1016/j.omtn.2019.09.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/26/2019] [Accepted: 09/12/2019] [Indexed: 11/18/2022]
Abstract
Antisense oligomers and their analogs have been successfully utilized to silence gene expression for the treatment of many human diseases; however, the control of yeast’s virulence determinants has never been exploited before. In this sense, this work is based on the key hypothesis that if a pathogen’s genetic sequence is a determinant of virulence, it will be possible to synthesize a nucleic acid mimic based on antisense therapy (AST) that will bind to the mRNA produced, blocking its translation into protein and, consequently, reducing the pathogen virulence phenotype. EFG1 is an important determinant of virulence that is involved in the regulation of the Candida albicans switch from yeast to filamentous form. Thus, our main goal was to design and synthesize an antisense oligonucleotide (ASO) targeting the EFG1 mRNA and to validate its in vitro applicability. The results show that the anti-EFG1 2′-OMethylRNA (2′OMe) oligomer was able to significantly reduce the levels of EFG1 gene expression and of Efg1p protein translation (both approximately 60%), as well as effectively prevent filamentation of C. albicans cells (by 80%). Moreover, it was verified that anti-EFG1 2′OMe keeps the efficacy in different simulated human body fluids. Undeniably, this work provides potentially valuable information for future research into the management of Candida infections, regarding the development of a credible and alternative method to control C. albicans infections, based on AST methodology.
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Affiliation(s)
- Daniela Araújo
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Nuno Miguel Azevedo
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Ana Barbosa
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Carina Almeida
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; INIAV, IP-National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, 4485-655 Vila do Conde, Portugal
| | - Maria Elisa Rodrigues
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Mariana Henriques
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Sónia Silva
- LIBRO-Laboratório de Investigação em Biofilmes Rosário Oliveira, CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
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10
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Milho C, Andrade M, Vilas Boas D, Alves D, Sillankorva S. Antimicrobial assessment of phage therapy using a porcine model of biofilm infection. Int J Pharm 2018; 557:112-123. [PMID: 30590127 DOI: 10.1016/j.ijpharm.2018.12.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/03/2018] [Accepted: 12/04/2018] [Indexed: 12/17/2022]
Abstract
Antibiotic resistant bacterial communities persist in many types of wounds, chronic wounds in particular, in the form of biofilms. Biofilm formation is a major cause of severe infections and the main reason for a negative treatment outcome and slow healing progression. Chronic wounds are a silent epidemic essentially affecting people with co-morbid conditions such as diabetes and obesity and elderly persons particularly those with movement limitations. The development of complementary and alternative effective strategies to antibiotics for the treatment of chronic wounds is highly desired. Phage therapy constitutes a very promising approach in the control of topical microbial populations. In this work newly isolated phages were tested for their efficacy to control bacterial species that predominate in chronic wounds. Phage effectiveness was studied on 24-h old biofilms formed in polystyrene microplates and in porcine skin explants using two treatment approaches: individual phage and a cocktail of phages against four main pathogens commonly isolated from chronic wounds. The two models produced variations in the surface colonization ability, assessed by viable bacterial counts and microscopy visualization after using peptide nucleic acid (PNA) or locked nucleic acid probes (LNA) and 2'-O-methyl (2'-OMe) in fluorescence in situ hybridization (FISH), and in the phage-host interactions. Phages alone and combined caused greater reductions in the number of viable cells when biofilms had been formed on porcine skins and with greater variations detected at 4 h and 24 h of sampling. These results suggest that porcine skin models should be preferentially used to assess the use of phages and phage cocktails intended for topical use in order to understand the fate, throughout treatment time, of the population when dealing with biofilm-related infections.
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Affiliation(s)
- C Milho
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - M Andrade
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - D Vilas Boas
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - D Alves
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal
| | - S Sillankorva
- Centre of Biological Engineering, LIBRO - Laboratório de Investigação em Biofilmes Rosário Oliveira, University of Minho, 4710-057 Braga, Portugal.
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11
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Rocha R, Sousa JM, Cerqueira L, Vieira MJ, Almeida C, Azevedo NF. Development and application of Peptide Nucleic Acid Fluorescence in situ Hybridization for the specific detection of Listeria monocytogenes. Food Microbiol 2018; 80:1-8. [PMID: 30704592 DOI: 10.1016/j.fm.2018.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 02/25/2018] [Accepted: 12/14/2018] [Indexed: 02/07/2023]
Abstract
Listeria monocytogenes is one of the most important foodborne pathogens due to the high hospitalization and mortality rates associated to an outbreak. Several new molecular methods that accelerate the identification of L. monocytogenes have been developed, however conventional culture-based methods still remain the gold standard. In this work we developed a novel Peptide Nucleic Acid Fluorescence in situ Hybridization (PNA-FISH) method for the specific detection of L. monocytogenes. The method was based on an already existing PNA probe, LmPNA1253, coupled with a novel blocker probe in a 1:2 ratio. The method was optimized for the detection of L. monocytogenes in food samples through an evaluation of several rich and selective enrichment broths. The best outcome was achieved using One Broth Listeria in a two-step enrichment of 24 h plus 18 h. For validation in food samples, ground beef, ground pork, milk, lettuce and cooked shrimp were artificially contaminated with two ranges of inoculum: a low level (0.2-2 CFU/25 g or mL) and a high level (2-10 CFU/25 g or mL). The PNA-FISH method performed well in all types of food matrices, presenting an overall accuracy of ≈99% and a detection limit of 0.5 CFU/25 g or mL of food sample.
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Affiliation(s)
- Rui Rocha
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal; CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; BIOMODE, Biomolecular Determination S.A., Edifício GNRATION, Praça Conde Agrolongo no 123, 4700-312, Braga, Portugal.
| | - José M Sousa
- BIOMODE, Biomolecular Determination S.A., Edifício GNRATION, Praça Conde Agrolongo no 123, 4700-312, Braga, Portugal
| | - Laura Cerqueira
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal; BIOMODE, Biomolecular Determination S.A., Edifício GNRATION, Praça Conde Agrolongo no 123, 4700-312, Braga, Portugal
| | - Maria J Vieira
- CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Carina Almeida
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal; CEB - Centre of Biological Engineering, LIBRO - Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal; BIOMODE, Biomolecular Determination S.A., Edifício GNRATION, Praça Conde Agrolongo no 123, 4700-312, Braga, Portugal; INIAV, IP- National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, 4485-655, Vairão, Vila do Conde, Portugal
| | - Nuno F Azevedo
- LEPABE, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal
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12
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Müller V, Sousa JM, Ceylan Koydemir H, Veli M, Tseng D, Cerqueira L, Ozcan A, Azevedo NF, Westerlund F. Identification of pathogenic bacteria in complex samples using a smartphone based fluorescence microscope. RSC Adv 2018; 8:36493-36502. [PMID: 35558922 PMCID: PMC9088845 DOI: 10.1039/c8ra06473c] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/21/2018] [Indexed: 11/21/2022] Open
Abstract
Diagnostics based on fluorescence imaging of biomolecules is typically performed in well-equipped laboratories and is in general not suitable for remote and resource limited settings. Here we demonstrate the development of a compact, lightweight and cost-effective smartphone-based fluorescence microscope, capable of detecting signals from fluorescently labeled bacteria. By optimizing a peptide nucleic acid (PNA) based fluorescence in situ hybridization (FISH) assay, we demonstrate the use of the smartphone-based microscope for rapid identification of pathogenic bacteria. We evaluated the use of both a general nucleic acid stain as well as species-specific PNA probes and demonstrated that the mobile platform can detect bacteria with a sensitivity comparable to that of a conventional fluorescence microscope. The PNA-based FISH assay, in combination with the smartphone-based fluorescence microscope, allowed us to qualitatively analyze pathogenic bacteria in contaminated powdered infant formula (PIF) at initial concentrations prior to cultivation as low as 10 CFU per 30 g of PIF. Importantly, the detection can be done directly on the smartphone screen, without the need for additional image analysis. The assay should be straightforward to adapt for bacterial identification also in clinical samples. The cost-effectiveness, field-portability and simplicity of this platform will create various opportunities for its use in resource limited settings and point-of-care offices, opening up a myriad of additional applications based on other fluorescence-based diagnostic assays. A smartphone-based fluorescence microscope for detection of bacteria in complex samples using a species-specific peptide nucleic acid probe.![]()
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
| | | | - Hatice Ceylan Koydemir
- Electrical and Computer Engineering Department
- University of California
- Los Angeles
- USA
- Bioengineering Department
| | - Muhammed Veli
- Electrical and Computer Engineering Department
- University of California
- Los Angeles
- USA
- Bioengineering Department
| | - Derek Tseng
- Electrical and Computer Engineering Department
- University of California
- Los Angeles
- USA
- Bioengineering Department
| | | | - Aydogan Ozcan
- Electrical and Computer Engineering Department
- University of California
- Los Angeles
- USA
- Bioengineering Department
| | - Nuno F. Azevedo
- LEPABE
- Department of Chemical Engineering
- Faculty of Engineering of the University of Porto
- 4200-465 Porto
- Portugal
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering
- Chalmers University of Technology
- Gothenburg
- Sweden
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13
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Scharinger EJ, Dietrich R, Wittwer T, Märtlbauer E, Schauer K. Multiplexed Lateral Flow Test for Detection and Differentiation of Cronobacter sakazakii Serotypes O1 and O2. Front Microbiol 2017; 8:1826. [PMID: 28979257 PMCID: PMC5611382 DOI: 10.3389/fmicb.2017.01826] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 09/06/2017] [Indexed: 01/28/2023] Open
Abstract
The ubiquitous and opportunistic pathogen Cronobacter sakazakii is responsible for severe meningitis, sepsis, and necrotizing enterocolitis in neonates and infants associated with ingestion of contaminated powdered infant formula (PIF). The current ISO method for isolation and detection of Cronobacter spp. is laborious, time-consuming and expensive. In this study, a multiplexed lateral flow test strip was developed to rapidly detect and simultaneously serotype O1 and O2 C. sakazakii serotypes. The assay is based on two monoclonal antibodies (MAb) that specifically bind to the lipopolysaccharides (LPS) of these pathogens. The test strip provides results very quickly; C. sakazakii could be detected in pure culture within 15 min with a sensitivity of 107 CFU/ml. After non-selective enrichment for 18 h as low as one Cronobacter cell per g PIF could be detected. Moreover, the established lateral flow assay (LFA) offers excellent specificity showing no cross-reactivity with other C. sakazakii serotypes, Cronobacter species or Enterobacteriaceae tested. These characteristics, together with several advantages such as speed, simplicity in performance, low analysis cost, and no requirement of specialized skills or sophisticated equipment make the developed multiplexed LFA suitable for reliable detection and serotyping of C. sakazakii serotypes O1 and O2.
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Affiliation(s)
- Eva J. Scharinger
- Department of Veterinary Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität MünchenOberschleißheim, Germany
| | - Richard Dietrich
- Department of Veterinary Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität MünchenOberschleißheim, Germany
| | | | - Erwin Märtlbauer
- Department of Veterinary Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität MünchenOberschleißheim, Germany
| | - Kristina Schauer
- Department of Veterinary Science, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität MünchenOberschleißheim, Germany
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14
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Hu S, Yu Y, Wu X, Xia X, Xiao X, Wu H. Simultaneous detection and identification of pathogenic Cronobacter
species by high-resolution melting analysis in powdered infant formulas. INT J DAIRY TECHNOL 2017. [DOI: 10.1111/1471-0307.12410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shuangfang Hu
- School of Food Science and Engineering; South China University of Technology; Guangzhou Guangdong 510640 China
| | - Yigang Yu
- School of Food Science and Engineering; South China University of Technology; Guangzhou Guangdong 510640 China
| | - Xinwei Wu
- Department of Microbiology; Guangzhou Center for Disease Control and Prevention; Qide Road No. 2 Guangzhou Guangdong 510440 China
| | - Xingzhou Xia
- College of Food Science and Technology; Guangdong Ocean University; Zhanjiang Guangdong 524088 China
| | - Xinglong Xiao
- School of Food Science and Engineering; South China University of Technology; Guangzhou Guangdong 510640 China
| | - Hui Wu
- School of Food Science and Engineering; South China University of Technology; Guangzhou Guangdong 510640 China
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Machado A, Cerca N. Multiplex Peptide Nucleic Acid Fluorescence In Situ Hybridization (PNA-FISH) for Diagnosis of Bacterial Vaginosis. Methods Mol Biol 2017; 1616:209-219. [PMID: 28600771 DOI: 10.1007/978-1-4939-7037-7_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Fluorescence in situ hybridization (FISH) is a molecular method used to identify and quantify microorganisms in a wide range of samples. This technique combines the simplicity of microscopic observation and the specificity of DNA/rRNA hybridization, allowing detection of selected bacterial species and morphologic visualization. Here, we describe a quantitative molecular diagnosis of bacterial vaginosis, based on the classical Nugent score. Our probes are able to differentiate Lactobacillus spp. and Gardnerella vaginalis from the other undefined bacterial species considered in the Nugent score.
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Affiliation(s)
- Antonio Machado
- Microbiology Institute, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Cumbayá, Quito, 170157, Ecuador
| | - Nuno Cerca
- CEB-Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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16
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Hu S, Yu Y, Li R, Wu X, Xiao X, Wu H. Rapid detection of Cronobacter sakazakii by real-time PCR based on the cgcA gene and TaqMan probe with internal amplification control. Can J Microbiol 2016; 62:191-200. [DOI: 10.1139/cjm-2015-0602] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cronobacter sakazakii is a severe virulent strain that is frequently detected in powdered infant formula (PIF). Therefore, it is necessary to develop a fast and specific detection method. The specificity of our newly developed quantitative real-time PCR (qRT–PCR) was validated with DNA from 46 strains. Among them, 12 C. sakazakii strains were correctly amplified, whereas no positive florescent signal was observed from 34 nontarget controls. The detection limit of C. sakazakii was about 110 CFU/mL in broth and 1100 CFU/g in PIF. After enrichment in buffered peptone water for 6 h, our developed qRT–PCR assay could reliably detect C. sakazakii when the inoculation level was as low as 2 CFU/25 g (0.08 CFU/g) in PIF. The growth of C. sakazakii could be inhibited by the presence of Lactobacillus pentosus and Bacillus cereus, which used a longer enrichment period before the isolation was accomplished. However, at 5 and 50 CFU/25 g inoculation levels of C. sakazakii in the presence of 4 × 106 CFU L. pentosus/25 g or of 2 × 104 CFU B. cereus/25 g, the qRT–PCR assay could detect the presence of Cronobacter even though these artificially spiked samples were negative in culture. Therefore, our results indicated that the qRT–PCR assay could detect samples containing inhibitors and could avoid false negatives by using an internal amplification control.
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Affiliation(s)
- Shuangfang Hu
- Research Center of Food Safety and Detection, College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou City, Guangdong Province 510640, People’s Republic of China
| | - Yigang Yu
- Research Center of Food Safety and Detection, College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou City, Guangdong Province 510640, People’s Republic of China
| | - Rong Li
- Zhongshan Entry-Exit Inspection and Quarantine Bureau, Room 804, No. 2, Zhongshan 6th Road, Zhongshan, Guangdong Province 528403, People’s Republic of China
| | - Xinwei Wu
- Department of Microbiology, Guangzhou Center for Disease Control and Prevention, Qide Road No. 2, Guangzhou, Guangdong Province 510440, People’s Republic of China
| | - Xinglong Xiao
- Research Center of Food Safety and Detection, College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou City, Guangdong Province 510640, People’s Republic of China
| | - Hui Wu
- Research Center of Food Safety and Detection, College of Light Industry and Food Sciences, South China University of Technology, 381 Wushan Road, Tianhe District, Guangzhou City, Guangdong Province 510640, People’s Republic of China
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Thung I, Aramin H, Vavinskaya V, Gupta S, Park JY, Crowe SE, Valasek MA. Review article: the global emergence of Helicobacter pylori antibiotic resistance. Aliment Pharmacol Ther 2016; 43:514-33. [PMID: 26694080 PMCID: PMC5064663 DOI: 10.1111/apt.13497] [Citation(s) in RCA: 495] [Impact Index Per Article: 61.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/04/2015] [Accepted: 11/19/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Helicobacter pylori is one of the most prevalent global pathogens and can lead to gastrointestinal disease including peptic ulcers, gastric marginal zone lymphoma and gastric carcinoma. AIM To review recent trends in H. pylori antibiotic resistance rates, and to discuss diagnostics and treatment paradigms. METHODS A PubMed literature search using the following keywords: Helicobacter pylori, antibiotic resistance, clarithromycin, levofloxacin, metronidazole, prevalence, susceptibility testing. RESULTS The prevalence of bacterial antibiotic resistance is regionally variable and appears to be markedly increasing with time in many countries. Concordantly, the antimicrobial eradication rate of H. pylori has been declining globally. In particular, clarithromycin resistance has been rapidly increasing in many countries over the past decade, with rates as high as approximately 30% in Japan and Italy, 50% in China and 40% in Turkey; whereas resistance rates are much lower in Sweden and Taiwan, at approximately 15%; there are limited data in the USA. Other antibiotics show similar trends, although less pronounced. CONCLUSIONS Since the choice of empiric therapies should be predicated on accurate information regarding antibiotic resistance rates, there is a critical need for determination of current rates at a local scale, and perhaps in individual patients. Such information would not only guide selection of appropriate empiric antibiotic therapy but also inform the development of better methods to identify H. pylori antibiotic resistance at diagnosis. Patient-specific tailoring of effective antibiotic treatment strategies may lead to reduced treatment failures and less antibiotic resistance.
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Affiliation(s)
- I. Thung
- Division of Anatomic PathologyDepartment of PathologyUniversity of California San Diego Medical CenterSan DiegoCAUSA
| | - H. Aramin
- Division of Anatomic PathologyDepartment of PathologyUniversity of California San Diego Medical CenterSan DiegoCAUSA
| | - V. Vavinskaya
- Division of Anatomic PathologyDepartment of PathologyUniversity of California San Diego Medical CenterSan DiegoCAUSA
| | - S. Gupta
- Division of GastroenterologyDepartment of MedicineUniversity of California San Diego Medical CenterLa JollaCAUSA
| | - J. Y. Park
- Department of Pathology and the Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical Center and Children's Medical CenterDallasTXUSA
| | - S. E. Crowe
- Division of GastroenterologyDepartment of MedicineUniversity of California San Diego Medical CenterLa JollaCAUSA
| | - M. A. Valasek
- Division of Anatomic PathologyDepartment of PathologyUniversity of California San Diego Medical CenterSan DiegoCAUSA
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18
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Vilas Boas D, Almeida C, Sillankorva S, Nicolau A, Azeredo J, Azevedo NF. Discrimination of bacteriophage infected cells using locked nucleic acid fluorescent in situ hybridization (LNA-FISH). BIOFOULING 2016; 32:179-190. [PMID: 26813295 DOI: 10.1080/08927014.2015.1131821] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/04/2015] [Indexed: 06/05/2023]
Abstract
Bacteriophage-host interaction studies in biofilm structures are still challenging due to the technical limitations of traditional methods. The aim of this study was to provide a direct fluorescence in situ hybridization (FISH) method based on locked nucleic acid (LNA) probes, which targets the phage replication phase, allowing the study of population dynamics during infection. Bacteriophages specific for two biofilm-forming bacteria, Pseudomonas aeruginosa and Acinetobacter, were selected. Four LNA probes were designed and optimized for phage-specific detection and for bacterial counterstaining. To validate the method, LNA-FISH counts were compared with the traditional plaque forming unit (PFU) technique. To visualize the progression of phage infection within a biofilm, colony-biofilms were formed and infected with bacteriophages. A good correlation (r = 0.707) was observed between LNA-FISH and PFU techniques. In biofilm structures, LNA-FISH provided a good discrimination of the infected cells and also allowed the assessment of the spatial distribution of infected and non-infected populations.
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Affiliation(s)
- Diana Vilas Boas
- b Laboratory for Process, Environment, Biotechnology and Energy Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Carina Almeida
- a LIBRO -Laboratório de Investigação em Biofilmes Rosário Oliveira , Centre of Biological Engineering, University of Minho , Braga , Portugal
- b Laboratory for Process, Environment, Biotechnology and Energy Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Sanna Sillankorva
- a LIBRO -Laboratório de Investigação em Biofilmes Rosário Oliveira , Centre of Biological Engineering, University of Minho , Braga , Portugal
| | - Ana Nicolau
- b Laboratory for Process, Environment, Biotechnology and Energy Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Joana Azeredo
- b Laboratory for Process, Environment, Biotechnology and Energy Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Nuno F Azevedo
- b Laboratory for Process, Environment, Biotechnology and Energy Engineering (LEPABE), Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
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19
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Azevedo AS, Almeida C, Pereira B, Madureira P, Wengel J, Azevedo NF. Detection and discrimination of biofilm populations using locked nucleic acid/2′-O-methyl-RNA fluorescence in situ hybridization (LNA/2′OMe-FISH). Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.04.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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20
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Sanchez-Vizuete P, Orgaz B, Aymerich S, Le Coq D, Briandet R. Pathogens protection against the action of disinfectants in multispecies biofilms. Front Microbiol 2015; 6:705. [PMID: 26236291 PMCID: PMC4500986 DOI: 10.3389/fmicb.2015.00705] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/26/2015] [Indexed: 01/09/2023] Open
Abstract
Biofilms constitute the prevalent way of life for microorganisms in both natural and man-made environments. Biofilm-dwelling cells display greater tolerance to antimicrobial agents than those that are free-living, and the mechanisms by which this occurs have been investigated extensively using single-strain axenic models. However, there is growing evidence that interspecies interactions may profoundly alter the response of the community to such toxic exposure. In this paper, we propose an overview of the studies dealing with multispecies biofilms resistance to biocides, with particular reference to the protection of pathogenic species by resident surface flora when subjected to disinfectants treatments. The mechanisms involved in such protection include interspecies signaling, interference between biocides molecules and public goods in the matrix, or the physiology and genetic plasticity associated with a structural spatial arrangement. After describing these different mechanisms, we will discuss the experimental methods available for their analysis in the context of complex multispecies biofilms.
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Affiliation(s)
- Pilar Sanchez-Vizuete
- INRA, UMR1319 MICALIS, Jouy-en-JosasFrance
- AgroParisTech, UMR MICALIS, Jouy-en-JosasFrance
| | - Belen Orgaz
- Department of Nutrition, Food Science and Technology, Faculty of Veterinary, Complutense University de MadridMadrid, Spain
| | - Stéphane Aymerich
- INRA, UMR1319 MICALIS, Jouy-en-JosasFrance
- AgroParisTech, UMR MICALIS, Jouy-en-JosasFrance
| | - Dominique Le Coq
- INRA, UMR1319 MICALIS, Jouy-en-JosasFrance
- AgroParisTech, UMR MICALIS, Jouy-en-JosasFrance
- CNRS, Jouy-en-JosasFrance
| | - Romain Briandet
- INRA, UMR1319 MICALIS, Jouy-en-JosasFrance
- AgroParisTech, UMR MICALIS, Jouy-en-JosasFrance
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21
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Almeida C, Constante D, Ferreira A, Cerqueira L, Vieira MJ, Azevedo NF. A new colorimetric peptide nucleic acid-based assay for the specific detection of bacteria. Future Microbiol 2015; 9:1131-42. [PMID: 25405883 DOI: 10.2217/fmb.14.68] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Developments on synthetic molecules, such as peptide nucleic acid (PNA), make FISH procedures more robust for microbial identification. Fluorochromes use might hinder a broader implementation of PNA-FISH, but colorimetric applications are inexistent so far. METHODS A biotin-labeled eubacteria probe was used to develop a colorimetric PNA-in situ hybridization (ISH) assay. An enzymatic-conjugate, targeting biotin, was introduced. The procedure was optimized and evaluated regarding sensitivity, specificity and detection limit. RESULTS RESULTS have shown strong ISH signals. The method was specific, but permeabilization problems were observed for Gram-positive bacteria. Detection limit was 5 × 10(7) CFU/ml, limiting current applications to pre-enriched samples. CONCLUSION The PNA-ISH procedure described here is a simple alternative to other detection methods, and is also the base for the development of other PNA colorimetric systems.
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Affiliation(s)
- Carina Almeida
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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Rohde A, Hammerl JA, Appel B, Dieckmann R, Al Dahouk S. FISHing for bacteria in food – A promising tool for the reliable detection of pathogenic bacteria? Food Microbiol 2015; 46:395-407. [DOI: 10.1016/j.fm.2014.09.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/15/2014] [Accepted: 09/05/2014] [Indexed: 12/28/2022]
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Machado A, Castro J, Cereija T, Almeida C, Cerca N. Diagnosis of bacterial vaginosis by a new multiplex peptide nucleic acid fluorescence in situ hybridization method. PeerJ 2015; 3:e780. [PMID: 25737820 PMCID: PMC4338769 DOI: 10.7717/peerj.780] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 01/30/2015] [Indexed: 11/20/2022] Open
Abstract
Bacterial vaginosis (BV) is one of most common vaginal infections. However, its diagnosis by classical methods reveals low specificity. Our goal was to evaluate the accuracy diagnosis of 150 vaginal samples with research gold standard methods and our Peptide Nucleic Acid (PNA) probes by Fluorescence in situ Hybridization (FISH) methodology. Also, we described the first PNA-FISH methodology for BV diagnosis, which provides results in approximately 3 h. The results showed a sensitivity of 84.6% (95% confidence interval (CI), from 64.3 to 95.0%) and a specificity of 97.6% (95% CI [92.6-99.4%]), demonstrating the higher specificity of the PNA-FISH method and showing false positive results in BV diagnosis commonly obtained by the classical methods. This methodology combines the specificity of PNA probes for Lactobacillus species and G. vaginalis visualization and the calculation of the microscopic field by Nugent score, allowing a trustful evaluation of the bacteria present in vaginal microflora and avoiding the occurrence of misleading diagnostics. Therefore, the PNA-FISH methodology represents a valuable alternative for BV diagnosis.
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Affiliation(s)
- António Machado
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| | - Joana Castro
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| | - Tatiana Cereija
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| | - Carina Almeida
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
| | - Nuno Cerca
- Centre of Biological Engineering, LIBRO-Laboratory of Research in Biofilms Rosário Oliveira, University of Minho , Campus de Gualtar, Braga , Portugal
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Kong D, Liu L, Xing C, Kuang H, Xu C. Sensitive and highly specific detection ofCronobacter sakazakiibased on monoclonal sandwich ELISA. FOOD AGR IMMUNOL 2015. [DOI: 10.1080/09540105.2014.998634] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Danko AS, Fontenete SJ, de Aquino Leite D, Leitão PO, Almeida C, Schaefer CE, Vainberg S, Steffan RJ, Azevedo NF. Detection of Dehalococcoides spp. by peptide nucleic acid fluorescent in situ hybridization. J Mol Microbiol Biotechnol 2014; 24:142-9. [PMID: 24970105 DOI: 10.1159/000362790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chlorinated solvents including tetrachloroethene (perchloroethene and trichloroethene), are widely used industrial solvents. Improper use and disposal of these chemicals has led to a widespread contamination. Anaerobic treatment technologies that utilize Dehalococcoides spp. can be an effective tool to remediate these contaminated sites. Therefore, the aim of this study was to develop, optimize and validate peptide nucleic acid (PNA) probes for the detection of Dehalococcoides spp. in both pure and mixed cultures. PNA probes were designed by adapting previously published DNA probes targeting the region of the point mutations described for discriminating between the Dehalococcoides spp. strain CBDB1 and strain 195 lineages. Different fixation, hybridization and washing procedures were tested. The results indicated that the PNA probes hybridized specifically and with a high sensitivity to their corresponding lineages, and that the PNA probes developed during this work can be used in a duplex assay to distinguish between strain CBDB1 and strain 195 lineages, even in complex mixed cultures. This work demonstrates the effectiveness of using PNA fluorescence in situ hybridization to distinguish between two metabolically and genetically distinct Dehalococcoides strains, and they can have strong implications in the monitoring and differentiation of Dehalococcoides populations in laboratory cultures and at contaminated sites.
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Affiliation(s)
- Anthony S Danko
- Centro de Investigação em Geo-Ambiente e Recursos (CIGAR), Departamento de Engenharia de Minas, Faculdade de Engenharia, Porto, Portugal
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Zhao Y, Yao Y, Xiao M, Chen Y, Lee CC, Zhang L, Zhang KX, Yang S, Gu M. Rapid detection of Cronobacter sakazakii in dairy food by biofunctionalized magnetic nanoparticle based on nuclear magnetic resonance. Food Control 2013. [DOI: 10.1016/j.foodcont.2013.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Detection of Escherichia coli O157 by peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) and comparison to a standard culture method. Appl Environ Microbiol 2013; 79:6293-300. [PMID: 23934486 DOI: 10.1128/aem.01009-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Despite the emergence of non-O157 Shiga toxin-producing Escherichia coli (STEC) infections, E. coli serotype O157 is still the most commonly identified STEC in the world. It causes high morbidity and mortality and has been responsible for a number of outbreaks in many parts of the world. Various methods have been developed to detect this particular serotype, but standard bacteriological methods remain the gold standard. Here, we propose a new peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) method for the rapid detection of E. coli O157. Testing on 54 representative strains showed that the PNA probe is highly sensitive and specific to E. coli O157. The method then was optimized for detection in food samples. Ground beef and unpasteurized milk samples were artificially contaminated with E. coli O157 concentrations ranging from 1 × 10(-2) to 1 × 10(2) CFU per 25 g or ml of food. Samples were then preenriched and analyzed by both the traditional bacteriological method (ISO 16654:2001) and PNA-FISH. The PNA-FISH method performed well in both types of food matrices with a detection limit of 1 CFU/25 g or ml of food samples. Tests on 60 food samples have shown a specificity value of 100% (95% confidence interval [CI], 82.83 to 100), a sensitivity of 97.22% (95% CI, 83.79 to 99.85%), and an accuracy of 98.33% (CI 95%, 83.41 to 99.91%). Results indicate that PNA-FISH performed as well as the traditional culture methods and can reduce the diagnosis time to 1 day.
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Machado A, Almeida C, Salgueiro D, Henriques A, Vaneechoutte M, Haesebrouck F, Vieira MJ, Rodrigues L, Azevedo NF, Cerca N. Fluorescence in situ Hybridization method using Peptide Nucleic Acid probes for rapid detection of Lactobacillus and Gardnerella spp. BMC Microbiol 2013; 13:82. [PMID: 23586331 PMCID: PMC3637831 DOI: 10.1186/1471-2180-13-82] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/27/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial vaginosis (BV) is a common vaginal infection occurring in women of reproductive age. It is widely accepted that the microbial switch from normal microflora to BV is characterized by a decrease in vaginal colonization by Lactobacillus species together with an increase of Gardnerella vaginalis and other anaerobes. Our goal was to develop and optimize a novel Peptide Nucleic Acid (PNA) Fluorescence in situ Hybridization assay (PNA FISH) for the detection of Lactobacillus spp. and G. vaginalis in mixed samples. RESULTS Therefore, we evaluated and validated two specific PNA probes by using 36 representative Lactobacillus strains, 22 representative G. vaginalis strains and 27 other taxonomically related or pathogenic bacterial strains commonly found in vaginal samples. The probes were also tested at different concentrations of G. vaginalis and Lactobacillus species in vitro, in the presence of a HeLa cell line. Specificity and sensitivity of the PNA probes were found to be 98.0% (95% confidence interval (CI), from 87.8 to 99.9%) and 100% (95% CI, from 88.0 to 100.0%), for Lactobacillus spp.; and 100% (95% CI, from 92.8 to 100%) and 100% (95% CI, from 81.5 to 100.0%) for G. vaginalis. Moreover, the probes were evaluated in mixed samples mimicking women with BV or normal vaginal microflora, demonstrating efficiency and applicability of our PNA FISH. CONCLUSIONS This quick method accurately detects Lactobacillus spp. and G. vaginalis species in mixed samples, thus enabling efficient evaluation of the two bacterial groups, most frequently encountered in the vagina.
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Affiliation(s)
- António Machado
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga 4710-057, Portugal
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Machado A, Almeida C, Carvalho A, Boyen F, Haesebrouck F, Rodrigues L, Cerca N, Azevedo NF. Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of Lactobacillus spp. in milk samples. Int J Food Microbiol 2013; 162:64-70. [PMID: 23357093 DOI: 10.1016/j.ijfoodmicro.2012.09.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 09/11/2012] [Accepted: 09/30/2012] [Indexed: 10/27/2022]
Abstract
Lactobacillus species constitute one of the dominant and beneficial bacteria in our body and are used in developed countries as a microbial adjuvant. Identification of these probiotic bacteria is traditionally performed by culture-based techniques. However, such methods are very time-consuming and can give inaccurate results, especially when Lactobacillus is present in mixed bacterial complex communities. Our study aimed to accurately identify Lactobacillus spp. using a novel Peptide Nucleic Acid (PNA) Fluorescence In Situ Hybridization (FISH) probe. The probe (Lac663) was tested on 36 strains belonging to different Lactobacillus species and on 20 strains of other bacterial species. The sensitivity and specificity of the method were 100% (95% confidence interval (CI), 88.0 to 100.0%) and 95.0% (95% CI, 73.1 to 99.7%), respectively. Additionally, we tested the applicability of the method on milk samples added with Lactobacillus strains at probiotic range concentrations and other taxonomically related bacteria, as well as pathogenic bacteria. The Lac663 probe bound exclusively to Lactobacillus strains and the described PNA-FISH method was capable of directly quantifying Lactobacillus spp. in concentrations at which these potential probiotic bacteria are considered to have an effective benefit on human health.
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Affiliation(s)
- Antonio Machado
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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30
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Almeida C, Azevedo NF, Bento JC, Cerca N, Ramos H, Vieira MJ, Keevil CW. Rapid detection of urinary tract infections caused by Proteus spp. using PNA-FISH. Eur J Clin Microbiol Infect Dis 2013; 32:781-6. [PMID: 23288291 DOI: 10.1007/s10096-012-1808-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 12/18/2012] [Indexed: 11/25/2022]
Abstract
We developed a fluorescence in situ hybridization (FISH) method for the rapid detection of Proteus spp. in urine, using a novel peptide nucleic acid (PNA) probe. Testing on 137 urine samples from patients with urinary tract infections has shown specificity and sensitivity values of 98 % (95 % CI, 93.2-99.7) and 100 % (95 % CI, 80,8-100), respectively, when compared with CHROMagar Orientation medium. Results indicate that PNA-FISH is a reliable alternative to traditional culture methods and can reduce the diagnosis time to approximately 2 h.
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Affiliation(s)
- C Almeida
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
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31
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Song KY, Chon JW, Kim HS, Seo KH. Current Cronobacter spp. Researches on Prevalence, Control, and Detection. ACTA ACUST UNITED AC 2012. [DOI: 10.7845/kjm.2012.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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32
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Yan QQ, Condell O, Power K, Butler F, Tall BD, Fanning S. Cronobacter species (formerly known as Enterobacter sakazakii) in powdered infant formula: a review of our current understanding of the biology of this bacterium. J Appl Microbiol 2012; 113:1-15. [PMID: 22420458 DOI: 10.1111/j.1365-2672.2012.05281.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cronobacter species (formerly known as Enterobacter sakazakii) are opportunistic pathogens that can cause necrotizing enterocolitis, bacteraemia and meningitis, predominantly in neonates. Infection in these vulnerable infants has been linked to the consumption of contaminated powdered infant formula (PIF). Considerable research has been undertaken on this organism in the past number of years which has enhanced our understanding of this neonatal pathogen leading to improvements in its control within the PIF production environment. The taxonomy of the organism resulted in the recognition of a new genus, Cronobacter, which consists of seven species. This paper presents an up-to-date review of our current knowledge of Cronobacter species. Taxonomy, genome sequencing, current detection protocols and epidemiology are all discussed. In addition, consideration is given to the control of this organism in the manufacturing environment, as a first step towards reducing the occurrence of this pathogen in PIF.
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Affiliation(s)
- Q Q Yan
- UCD Centre for Food Safety, WHO Collaborating Centre for Research, Reference & Training on Cronobacter, School of Public Health, Physiotherapy & Population Science, University College Dublin, Dublin, Ireland
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33
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Norberg S, Stanton C, Ross RP, Hill C, Fitzgerald GF, Cotter PD. Cronobacter spp. in powdered infant formula. J Food Prot 2012; 75:607-20. [PMID: 22410240 DOI: 10.4315/0362-028x.jfp-11-285] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cronobacter species are opportunistic pathogens, and a mortality rate of 40 to 80% is associated with infections. This pathogen can cause a range of serious diseases such as meningitis, septicemia, necrotizing enterocolitis, and brain abscesses and has been responsible for a variety of sequelae such as quadriplegia. Although Cronobacter can cause disease in both adults and infants, infant infections associated with powdered formula are the focus of this review. Since the first reported Cronobacter infection outbreak in 1958, powdered infant formula has been identified as a major source of these outbreaks, resulting in many recalls of powdered infant formula worldwide. This contamination has created an immense problem for the powdered infant formula industry. In this review, we discuss the taxonomy of Cronobacter species, the natural habitat of Cronobacter and its presence in foods, the physiology, pathogenicity, and virulence of Cronobacter species, and available detection methods. We also discuss reported cases of Cronobacter infection linked to powdered infant formula consumption and then focus specifically on the official World Health Organization guidelines for preparation of powdered infant formula.
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Affiliation(s)
- Sarah Norberg
- Department of Microbiology, University College Cork, Cork, Ireland
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Azevedo NF, Jardim T, Almeida C, Cerqueira L, Almeida AJ, Rodrigues F, Keevil CW, Vieira MJ. Application of flow cytometry for the identification of Staphylococcus epidermidis by peptide nucleic acid fluorescence in situ hybridization (PNA FISH) in blood samples. Antonie van Leeuwenhoek 2011; 100:463-70. [PMID: 21638111 DOI: 10.1007/s10482-011-9595-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 05/20/2011] [Indexed: 11/28/2022]
Abstract
Staphylococcus epidermidis is considered to be one of the most common causes of nosocomial bloodstream infections, particularly in immune-compromised individuals. Here, we report the development and application of a novel peptide nucleic acid probe for the specific detection of S. epidermidis by fluorescence in situ hybridization. The theoretical estimates of probe matching specificity and sensitivity were 89 and 87%, respectively. More importantly, the probe was shown not to hybridize with closely related species such as Staphylococcus aureus. The method was subsequently successfully adapted for the detection of S. epidermidis in mixed-species blood cultures both by microscopy and flow cytometry.
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Affiliation(s)
- N F Azevedo
- IBB, Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal.
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Cerqueira L, Fernandes RM, Ferreira RM, Carneiro F, Dinis-Ribeiro M, Figueiredo C, Keevil CW, Azevedo NF, Vieira MJ. PNA-FISH as a new diagnostic method for the determination of clarithromycin resistance of Helicobacter pylori. BMC Microbiol 2011; 11:101. [PMID: 21569555 PMCID: PMC3112065 DOI: 10.1186/1471-2180-11-101] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/14/2011] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Triple therapy is the gold standard treatment for Helicobacter pylori eradication from the human stomach, but increased resistance to clarithromycin became the main factor of treatment failure. Until now, fastidious culturing methods are generally the method of choice to assess resistance status. In this study, a new genotypic method to detect clarithromycin resistance in clinical samples, based on fluorescent in situ hybridization (FISH) using a set of peptide nucleic acid probes (PNA), is proposed. RESULTS The set of probes targeting the point mutations responsible for clarithromycin resistance was applied to H. pylori suspensions and showed 100% sensitivity and specificity (95% CI, 79.9-100 and 95% CI, 71.6-100 respectively). This method can also be amenable for application to gastric biopsy samples, as resistance to clarithromycin was also detected when histological slides were tested. CONCLUSIONS The optimized PNA-FISH based diagnostic method to detect H. pylori clarithromycin resistance shown to be a very sensitive and specific method for the detection of clarithromycin resistance in the H. pylori smears and also proved to be a reliable method for the diagnosis of this pathogen in clinical samples and an alternative to existing plating methods.
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Affiliation(s)
- Laura Cerqueira
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal
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Almeida C, Azevedo NF, Santos S, Keevil CW, Vieira MJ. Discriminating multi-species populations in biofilms with peptide nucleic acid fluorescence in situ hybridization (PNA FISH). PLoS One 2011; 6:e14786. [PMID: 21479268 PMCID: PMC3066202 DOI: 10.1371/journal.pone.0014786] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 10/11/2010] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Our current understanding of biofilms indicates that these structures are typically composed of many different microbial species. However, the lack of reliable techniques for the discrimination of each population has meant that studies focusing on multi-species biofilms are scarce and typically generate qualitative rather than quantitative data. METHODOLOGY/PRINCIPAL FINDINGS We employ peptide nucleic acid fluorescence in situ hybridization (PNA FISH) methods to quantify and visualize mixed biofilm populations. As a case study, we present the characterization of Salmonella enterica/Listeria monocytogenes/Escherichia coli single, dual and tri-species biofilms in seven different support materials. Ex-situ, we were able to monitor quantitatively the populations of ∼56 mixed species biofilms up to 48 h, regardless of the support material. In situ, a correct quantification remained more elusive, but a qualitative understanding of biofilm structure and composition is clearly possible by confocal laser scanning microscopy (CLSM) at least up to 192 h. Combining the data obtained from PNA FISH/CLSM with data from other established techniques and from calculated microbial parameters, we were able to develop a model for this tri-species biofilm. The higher growth rate and exopolymer production ability of E. coli probably led this microorganism to outcompete the other two [average cell numbers (cells/cm(2)) for 48 h biofilm: E. coli 2,1 × 10(8) (± 2,4 × 10(7)); L. monocytogenes 6,8 × 10(7) (± 9,4 × 10(6)); and S. enterica 1,4 × 10(6) (± 4,1 × 10(5))]. This overgrowth was confirmed by CSLM, with two well-defined layers being easily identified: the top one with E. coli, and the bottom one with mixed regions of L. monocytogenes and S. enterica. SIGNIFICANCE While PNA FISH has been described previously for the qualitative study of biofilm populations, the present investigation demonstrates that it can also be used for the accurate quantification and spatial distribution of species in polymicrobial communities. Thus, it facilitates the understanding of interspecies interactions and how these are affected by changes in the surrounding environment.
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Affiliation(s)
- Carina Almeida
- Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, Universidade do Minho, Campus de Gualta, Braga, Portugal
- Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Nuno F. Azevedo
- Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Sílvio Santos
- Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, Universidade do Minho, Campus de Gualta, Braga, Portugal
| | - Charles W. Keevil
- Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Maria J. Vieira
- Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, Universidade do Minho, Campus de Gualta, Braga, Portugal
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Blažková M, Javůrková B, Fukal L, Rauch P. Immunochromatographic strip test for detection of genus Cronobacter. Biosens Bioelectron 2010; 26:2828-34. [PMID: 21169009 DOI: 10.1016/j.bios.2010.10.001] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 09/17/2010] [Accepted: 10/02/2010] [Indexed: 12/11/2022]
Abstract
Members of the genus Cronobacter are opportunistic pathogens formerly known as Enterobacter sakazakii, which induce severe meningitis and sepsis in neonates and infants, with a high fatality rate. In this work, a simple and rapid immunochromatographic strip test for the detection of this pathogen was developed. Following the shortened bacteria cultivation and isolation of DNA, a specific gene sequence targeting 16S rRNA from Cronobacter spp. was amplified by PCR using 5'-end labelled specific primers. The PCR product, amplicon labelled with digoxigenin on one side and biotin on the other side, was directly added to the immunochromatographic strip test, composed of nitrocellulose membrane with bound antibody against digoxigenin in the test line. The visualization was mediated by colloidal carbon conjugated to neutravidin, and the appearance of grey/black line was indicative of the presence of specific amplicon. Colour intensity of the test line in pathogen-positive assay was visually distinguishable from that of negative sample within 10 min. The visual detection limit of PCR product was 8 ng. The specificity of the developed method was confirmed by standard microbiological techniques. Whole detection procedure with the incorporated immunostrip was applied to analysis of infant formulae samples, contaminated with less than 10 cells of Cronobacter spp. per 10 g. The results from immunochromatographic test indicated the absolute agreement with those from standard microbiological methods. Moreover, the developed procedure considerably reduced the total analysis time to 16 h whereas the reference microbiological method needs 6-7 days.
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Affiliation(s)
- Martina Blažková
- Department of Biochemistry and Microbiology, Institute of Chemical Technology, Technická 3, 166 28 Prague, Czech Republic
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38
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Almeida C, Azevedo NF, Fernandes RM, Keevil CW, Vieira MJ. Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of Salmonella spp. in a broad spectrum of samples. Appl Environ Microbiol 2010; 76:4476-85. [PMID: 20453122 PMCID: PMC2897454 DOI: 10.1128/aem.01678-09] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 10/20/2009] [Indexed: 11/20/2022] Open
Abstract
A fluorescence in situ hybridization (FISH) method for the rapid detection of Salmonella spp. using a novel peptide nucleic acid (PNA) probe was developed. The probe theoretical specificity and sensitivity were both 100%. The PNA-FISH method was optimized, and laboratory testing on representative strains from the Salmonella genus subspecies and several related bacterial species confirmed the predicted theoretical values of specificity and sensitivity. The PNA-FISH method has been successfully adapted to detect cells in suspension and is hence able to be employed for the detection of this bacterium in blood, feces, water, and powdered infant formula (PIF). The blood and PIF samples were artificially contaminated with decreasing pathogen concentrations. After the use of an enrichment step, the PNA-FISH method was able to detect 1 CFU per 10 ml of blood (5 x 10(9) +/- 5 x 10(8) CFU/ml after an overnight enrichment step) and also 1 CFU per 10 g of PIF (2 x 10(7) +/- 5 x 10(6) CFU/ml after an 8-h enrichment step). The feces and water samples were also enriched according to the corresponding International Organization for Standardization methods, and results showed that the PNA-FISH method was able to detect Salmonella immediately after the first enrichment step was conducted. Moreover, the probe was able to discriminate the bacterium in a mixed microbial population in feces and water by counter-staining with 4',6-diamidino-2-phenylindole (DAPI). This new method is applicable to a broad spectrum of samples and takes less than 20 h to obtain a diagnosis, except for PIF samples, where the analysis takes less than 12 h. This procedure may be used for food processing and municipal water control and also in clinical settings, representing an improved alternative to culture-based techniques and to the existing Salmonella PNA probe, Sal23S10, which presents a lower specificity.
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Affiliation(s)
- C. Almeida
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal, Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East SO16 7PX, Southampton, United Kingdom, LEPAE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - N. F. Azevedo
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal, Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East SO16 7PX, Southampton, United Kingdom, LEPAE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - R. M. Fernandes
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal, Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East SO16 7PX, Southampton, United Kingdom, LEPAE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - C. W. Keevil
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal, Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East SO16 7PX, Southampton, United Kingdom, LEPAE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - M. J. Vieira
- Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal, Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East SO16 7PX, Southampton, United Kingdom, LEPAE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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Healy B, Cooney S, O'Brien S, Iversen C, Whyte P, Nally J, Callanan JJ, Fanning S. Cronobacter (Enterobacter sakazakii): an opportunistic foodborne pathogen. Foodborne Pathog Dis 2010; 7:339-50. [PMID: 19958103 DOI: 10.1089/fpd.2009.0379] [Citation(s) in RCA: 196] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cronobacter spp. (Enterobacter sakazakii) are a recently described genus that is comprised of six genomospecies. The classification of these organisms was revised based on a detailed polyphasic taxonomic study. Cronobacter spp. are regarded as ubiquitous organisms having been isolated from a wide variety of foods. These bacteria are opportunistic pathogens and are linked with life-threatening infections in neonates. Clinical symptoms of Cronobacter infection include necrotizing enterocolitis, bacteremia, and meningitis, with case fatality rates of 50-80% being reported. Contaminated powdered infant formula has been epidemiologically linked with infections. Recently, infections among immunocompromised adults, mainly the elderly, have also been reported. A high tolerance to osmotic stress and elevated temperatures contribute to the survival of Cronobacter spp. in dried foods such as powdered infant formula. Controlling the organism in the production environment, thereby reducing dissemination, necessitates the provision of suitable diagnostic tools. Studies demonstrated that a high degree of variability exists amongst the phenotypic-based methods used to identify Cronobacter spp. However, advances in molecular detection and subtyping techniques have significantly improved the identification and characterization of Cronobacter spp. The dose required to induce infection has yet to be determined. In vitro virulence studies have shown that Cronobacter spp. may survive in macrophage cells and efficiently attach to and invade epithelial cell lines. The production of exopolysaccharide may contribute to the formation of biofilm and active efflux pumps promote resistance to antimicrobial agents such as bile salts and disinfectants. A holistic approach combining techniques such as comparative genome analysis, proteomics, and in vivo challenges could help unravel the complex interactions between this pathogen and its host. These data would help identify those properties in Cronobacter spp. which enable the bacterium to survive in the production environment and infect vulnerable neonates via the food chain.
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Affiliation(s)
- Brendan Healy
- Centres for Food Safety and Foodborne Zoonomics, School of Agriculture, Food Science, and Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland
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