1
|
Hortelano I, Moreno MY, García-Hernández J, Ferrús MA. Optimization of pre- treatments with Propidium Monoazide and PEMAX™ before real-time quantitative PCR for detection and quantification of viable Helicobacter pylori cells. J Microbiol Methods 2021; 185:106223. [PMID: 33872638 DOI: 10.1016/j.mimet.2021.106223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 12/17/2022]
Abstract
Accurate detection of H. pylori in different environmental and clinical samples is essential for public health strtdudies. Now, a big effort is being made to design PCR methodologies that allow for the detection of viable and viable but non-culturable (VBNC) H. pylori cells, by achieving complete exclusion of dead cells amplification signals. The use of DNA intercalating dyes has been proposed. However, its efficacy is still not well determined. In this study, we aimed to test the suitability of PMA and PEMAX™ dyes used prior to qPCR for only detecting viable cells of H. pylori. Their efficiency was evaluated with cells submitted to different disinfection treatments and confirmed by the absence of growth on culture media and by LIVE/DEAD counts. Our results indicated that an incubation period of 5 min for both, PMA and PEMAX™, did not affect viable cells. Our study also demonstrated that results obtained by using intercalating dyes may vary depending on the cell stress conditions. In all dead cell's samples, both PMA and PEMAX™ pre-qPCR treatments decreased the amplification signal (>103 Genomic Units (GU)), although none of them allowed for its disappearance confirming that intercalating dyes, although useful for screening purposes, cannot be considered as universal viability markers. To investigate the applicability of the method specifically to detect H. pylori cells in environmental samples, PMA-qPCR was performed on samples containing the different morphological and viability states that H. pylori can acquire in environment. The optimized PMA-qPCR methodology showed to be useful to detect mostly (but not only) viable forms, regardless the morphological state of the cell.
Collapse
Affiliation(s)
- Irene Hortelano
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, 46022, Valencia, Spain.
| | - María Yolanda Moreno
- Research Institute of Water and Environmental Engineering (IIAMA), Universitat Politècnica de València, 46022, Valencia, Spain
| | | | - María Antonia Ferrús
- Biotechnology Department, Universitat Politècnica de València, 46022, Valencia, Spain.
| |
Collapse
|
2
|
Guliy OI, Zaitsev BD, Mehta SK, Borodina IA. Analysis of Microbial Cell Viability in a Liquid Using an Acoustic Sensor. ULTRASOUND IN MEDICINE & BIOLOGY 2020; 46:1026-1039. [PMID: 31932157 DOI: 10.1016/j.ultrasmedbio.2019.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 12/05/2019] [Accepted: 12/06/2019] [Indexed: 06/10/2023]
Abstract
A method was developed for the rapid analysis and evaluation of the viability of bacteriophage-infected Escherichia coli (E.coli) XL-1 directly in a conducting suspension by using a slot-mode sensor. The method is based on recording the changes in the depth and frequency of resonant absorption peaks in the frequency dependence of the insertion loss of the sensor before and after the biologic interaction of E. coli with specific bacteriophages. The possibility was shown of recording the infection of E. coli with specific bacteriophages and assessing its viability in suspensions with a conductivity of 4.5-30 μS/cm. Сontrol experiments were carried out with non-specific interactions of E. coli cells with bacteriophages, in which no changes in the sensor variables were observed. The optimal informational variable for estimating the number of viable cells was the degree of change in the depth of the resonant peaks in the frequency dependence of the insertion loss of the sensor. The limit of cell detection was ∼102-103 cells mL-1, with an analysis time of about 5 min. An additional advantage of the sensor was the availability of a removable liquid container, which allows one to use it repeatedly and to facilitate the cleaning of the container from spent samples. The results are promising for the detection of bacteria and assessment of their viability in solutions with conductivity in the range 4.5-30 µS/cm.
Collapse
Affiliation(s)
- Olga I Guliy
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences Saratov, Russia.
| | - Boris D Zaitsev
- Kotelnikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Saratov, Russia
| | | | - Irina A Borodina
- Kotelnikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Saratov, Russia
| |
Collapse
|
3
|
Baymiev AK, Baymiev AK, Kuluev BR, Shvets KY, Yamidanov RS, Matniyazov RT, Chemeris DA, Zubov VV, Alekseev YI, Mavzyutov AR, Ivanenkov YA, Chemeris AV. Modern Approaches to Differentiation of Live and Dead Bacteria Using Selective Amplification of Nucleic Acids. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720010038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
|
4
|
Kumar SS, Ghosh AR. Assessment of bacterial viability: a comprehensive review on recent advances and challenges. Microbiology (Reading) 2019; 165:593-610. [DOI: 10.1099/mic.0.000786] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Shravanthi S. Kumar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Asit Ranjan Ghosh
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| |
Collapse
|
5
|
Acosta CP, Codony F, Fittipaldi M, Sierra-Torres CH, Morató J. Monitoring levels of viable Helicobacter pylori in surface water by qPCR in Northeast Spain. JOURNAL OF WATER AND HEALTH 2018; 16:839-845. [PMID: 30285964 DOI: 10.2166/wh.2018.195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Helicobacter pylori infection is a risk factor for chronic active gastritis, peptic ulcers, gastric carcinoma and lymphoma. Although the infection may be acquired through different transmission routes, the presence and viability of H. pylori in water sources are not well known. Therefore, the aim of our study was to analyse the viability of H. pylori cells in urban surface waters collected at the Vallparadís public park in Terrassa, Barcelona, Spain. The water samples were analysed by viability quantitative polymerase chain reaction (qPCR) using propidium monoazide and specific primers for the H. pylori vacuolating cytotoxin (vacA gene). Viable H. pylori were found in 91.3% of the samples analysed, with an average concentration of 3.46 ± 1.06 log cell 100 mL-1. Our work proves a quick and simple procedure for evaluating viable H. pylori cells in environmental samples by qPCR. Furthermore, the results provide evidence that urban surface waters may contain considerable levels of viable H. pylori cells, thus indicating they are a potential source of infection, which represents a public health concern.
Collapse
Affiliation(s)
- Claudia Patricia Acosta
- Laboratorio de Genética Humana, Departamento de Ciencias Fisiológicas, Facultad de Ciencias de la Salud, Universidad del Cauca, Popayán, Colombia and Unidad de Salud Ambiental, Fundación InnovaGen, Popayán, Colombia E-mail:
| | - Francesc Codony
- Laborati de Microbiologia Sanitària i Mediambiental (MSMLab) -Aquasoft, UNESCO Chair in Sustainability, Universitat Politècnica de Catalunya, Edifici Gala, Pg. Ernest Lluch/Rambla Sant Nebridi, Terrassa 08222, Barcelona, Spain; GenIUL R&D Laboratory, Edifici Gala, Pg. Ernest Lluch/Rambla Sant Nebridi, Terrassa, Spain
| | - Mariana Fittipaldi
- Laborati de Microbiologia Sanitària i Mediambiental (MSMLab) -Aquasoft, UNESCO Chair in Sustainability, Universitat Politècnica de Catalunya, Edifici Gala, Pg. Ernest Lluch/Rambla Sant Nebridi, Terrassa 08222, Barcelona, Spain
| | - Carlos Hernán Sierra-Torres
- Laboratorio de Genética Humana, Departamento de Ciencias Fisiológicas, Facultad de Ciencias de la Salud, Universidad del Cauca, Popayán, Colombia and Unidad de Salud Ambiental, Fundación InnovaGen, Popayán, Colombia E-mail:
| | - Jordi Morató
- Laborati de Microbiologia Sanitària i Mediambiental (MSMLab) -Aquasoft, UNESCO Chair in Sustainability, Universitat Politècnica de Catalunya, Edifici Gala, Pg. Ernest Lluch/Rambla Sant Nebridi, Terrassa 08222, Barcelona, Spain
| |
Collapse
|
6
|
Kaplan HB, Miranda JA, Gogola GR, Gomez K, Ambrose CG. Persistence of bacterial DNA in orthopedic infections. Diagn Microbiol Infect Dis 2018; 91:136-140. [PMID: 29467085 DOI: 10.1016/j.diagmicrobio.2018.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 01/10/2023]
Abstract
Polymerase chain reaction (PCR) has been proposed as a method to identify bacteria in clinical samples because it is more sensitive than culture techniques and can produce results rapidly. However, PCR can detect DNA from dead cells and thus cannot distinguish between live and dead cells in a tissue sample. Killed Staphylococcus aureus cells were implanted into the femurs and knee joints of rats to determine the length of time that DNA from dead cells is detectable in a living animal under conditions similar to common orthopedic infections. In the joint infection model studied here, the DNA from the dead planktonic bacteria was detected using PCR immediately after injection or 24 h later, but was undetectable 48 and 72 h after injection. In the biofilm implanted-device model studied, the DNA from these dead biofilm cells was detected by PCR immediately after implantation and at 24 h, but not at 48 or 72 h. Thus, our results indicate that DNA from dead cells does not persist in these animal model systems for more than 2 days, which should reduce concerns about possible false positive results using molecular DNA-based techniques for the detection of pathogens.
Collapse
Affiliation(s)
- Heidi B Kaplan
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX
| | - Justin A Miranda
- Department of Orthopaedic Surgery, University of Texas Health Science Center at Houston, Houston, TX
| | | | - Karen Gomez
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX
| | - Catherine G Ambrose
- Department of Orthopaedic Surgery, University of Texas Health Science Center at Houston, Houston, TX.
| |
Collapse
|
7
|
Tantikachornkiat M, Sakakibara S, Neuner M, Durall DM. The use of propidium monoazide in conjunction with qPCR and Illumina sequencing to identify and quantify live yeasts and bacteria. Int J Food Microbiol 2016; 234:53-59. [DOI: 10.1016/j.ijfoodmicro.2016.06.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 10/21/2022]
|
8
|
Heise J, Nega M, Alawi M, Wagner D. Propidium monoazide treatment to distinguish between live and dead methanogens in pure cultures and environmental samples. J Microbiol Methods 2015; 121:11-23. [PMID: 26656002 DOI: 10.1016/j.mimet.2015.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 12/02/2015] [Accepted: 12/02/2015] [Indexed: 11/16/2022]
Abstract
In clinical trials investigating human health and in the analysis of microbial communities in cultures and natural environments, it is a substantial challenge to differentiate between living, potentially active communities and dead cells. The DNA-intercalating dye propidium monoazide (PMA) enables the selective masking of DNA from dead, membrane-compromised cells immediately before DNA extraction. In the present study, we evaluated for the first time a PMA treatment for methanogenic archaea in cultures and particle-rich environmental samples. Using microscopic analyses, we confirmed the applicability of the LIVE/DEAD(®) BacLight™ kit to methanogenic archaea and demonstrated the maintenance of intact cell membranes of methanogens in the presence of PMA. Although strain-specific differences in the efficiency of PMA treatment to methanogenic archaea were observed, we developed an optimal procedure using 130 μM PMA and 5min of photo-activation with blue LED light. The results showed that the effectiveness of the PMA treatment strongly depends on the texture of the sediment/soil: silt and clay-rich sediments represent a challenge at all concentrations, whereas successful suppression of DNA from dead cells with compromised membranes was possible for low particle loads of sandy soil (total suspended solids (TSS)≤200 mg mL(-1)). Conclusively, we present two strategies to overcome the problem of insufficient light activation of PMA caused by the turbidity effect (shielding) in particle-rich environmental samples by (i) dilution of the particle-rich sample and (ii) detachment of the cells and the free DNA from the sediment prior to a PMA treatment. Both strategies promise to be usable options for distinguishing living cells and free DNA in complex environmental samples.
Collapse
Affiliation(s)
- Janine Heise
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Marcella Nega
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Mashal Alawi
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany.
| |
Collapse
|
9
|
Payne MS, Bayatibojakhi S. Exploring preterm birth as a polymicrobial disease: an overview of the uterine microbiome. Front Immunol 2014; 5:595. [PMID: 25505898 PMCID: PMC4245917 DOI: 10.3389/fimmu.2014.00595] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/06/2014] [Indexed: 02/04/2023] Open
Abstract
Infection is a leading cause of preterm birth (PTB). A focus of many studies over the past decade has been to characterize microorganisms present in the uterine cavity and document any association with negative pregnancy outcome. A range of techniques have been used to achieve this, including microbiological culture and targeted polymerase chain reaction assays, and more recently, microbiome-level analyses involving either conserved, phylogenetically informative genes such as the bacterial 16S rRNA gene or whole shotgun metagenomic sequencing. These studies have contributed vast amounts of data toward characterization of the uterine microbiome, specifically that present in the amniotic fluid, fetal membranes, and placenta. However, an overwhelming emphasis has been placed on the bacterial microbiome, with far less data produced on the viral and fungal/yeast microbiomes. With numerous studies now referring to PTB as a polymicrobial condition, there is the need to investigate the role of viruses and fungi/yeasts in more detail and in particular, look for associations between colonization with these microorganisms and bacteria in the same samples. Although the major pathway by which microorganisms are believed to colonize the uterine cavity is vertical ascension from the vagina, numerous studies are now emerging suggesting hematogenous transfer of oral microbiota to the uterine cavity. Evidence of this has been produced in mouse models and although DNA-based evidence in humans appears convincing in some aspects, use of methodologies that only detect viable cells as opposed to lysed cells and extracellular DNA are needed to clarify this. Such techniques as RNA analyses and viability polymerase chain reaction are likely to play key roles in the clinical translation of future microbiome-based data, particularly in confined environments such as the uterus, as detection of viable cells plays a key role in diagnosis and treatment of infection.
Collapse
Affiliation(s)
- Matthew S Payne
- School of Women's and Infants' Health, The University of Western Australia , Perth, WA , Australia
| | - Sara Bayatibojakhi
- School of Women's and Infants' Health, The University of Western Australia , Perth, WA , Australia
| |
Collapse
|
10
|
Rogers GB, van der Gast CJ, Bruce KD, Marsh P, Collins JE, Sutton J, Wright M. Ascitic microbiota composition is correlated with clinical severity in cirrhosis with portal hypertension. PLoS One 2013; 8:e74884. [PMID: 24086392 PMCID: PMC3783492 DOI: 10.1371/journal.pone.0074884] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 08/07/2013] [Indexed: 02/07/2023] Open
Abstract
Identification of pathogenic bacteria in ascites correlates with poor clinical outcomes. Ascites samples are commonly reported culture-negative, even where frank infection is indicated. Culture-independent methods have previously reported bacterial DNA in ascites, however, whether this represents viable bacterial populations has not been determined. We report the first application of 16S rRNA gene pyrosequencing and quantitative PCR in conjunction with propidium monoazide sample treatment to characterise the viable bacterial composition of ascites. Twenty five cirrhotic patients undergoing paracentesis provided ascites. Samples were treated with propidium monoazide to exclude non-viable bacterial DNA. Total bacterial load was quantified by 16S rRNA Q-PCR with species identity and relative abundance determined by 16S rRNA gene pyrosequencing. Correlation of molecular microbiology data with clinical measures and diagnostic microbiology was performed. Viable bacterial signal was obtained in 84% of ascites samples, both by Q-PCR and pyrosequencing. Approximately 190,000 ribosomal pyrosequences were obtained, representing 236 species, including both gut and non gut-associated species. Substantial variation in the species detected was observed between patients. Statistically significant relationships were identified between the bacterial community similarity and clinical measures, including ascitic polymorphonuclear leukocyte count and Child-Pugh class. Viable bacteria are present in the ascites of a majority of patients with cirrhosis including those with no clinical signs of infection. Microbiota composition significantly correlates with clinical measures. Entry of bacteria into ascites is unlikely to be limited to translocation from the gut, raising fundamental questions about the processes that underlie the development of spontaneous bacterial peritonitis.
Collapse
Affiliation(s)
- Geraint B. Rogers
- Institute of Pharmaceutical Science, King’s College London, London, United Kingdom
- * E-mail:
| | | | - Kenneth D. Bruce
- Institute of Pharmaceutical Science, King’s College London, London, United Kingdom
| | - Peter Marsh
- Health Protection Agency, Southampton General Hospital, Southampton, United Kingdom
| | - Jane E. Collins
- Hepatology Group, Southampton General Hospital, Southampton, United Kingdom
| | - Julian Sutton
- Health Protection Agency, Southampton General Hospital, Southampton, United Kingdom
| | - Mark Wright
- Hepatology Group, Southampton General Hospital, Southampton, United Kingdom
| |
Collapse
|
11
|
Chang CW, Lu LW, Kuo CL, Hung NT. Density of environmental Acanthamoeba and their responses to superheating disinfection. Parasitol Res 2013; 112:3687-96. [PMID: 23933810 DOI: 10.1007/s00436-013-3556-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 07/22/2013] [Indexed: 10/26/2022]
Abstract
Exposure to viable Acanthamoeba may cause fatal encephalitis and blinding keratitis in humans. Quantification of environmental Acanthamoeba by a reliable analytical assay is essential to assess the risk of human exposure and efficacy of control measures (e.g., superheating). Two DNA binding dyes (ethidium monoazide (EMA) and propidium monoazide) coupled with real-time quantitative PCR (qPCR) were tested for the ability in selectively quantifying viable Acanthamoeba castellanii. This newly developed qPCR assay was applied to determine the density of environmental Acanthamoeba and disinfection efficacy of superheating. Results showed qPCR with 2.3 μg/mL EMA performed optimal with a great linearity (R (2) = 0.98) and a wide range of detection (5-1.5 × 10(5) cells). EMA-qPCR analyses on water samples collected from cooling towers, eyewash stations, irrigated farmlands, and various wastewater treatment stages further showed viable Acanthamoeba density from nondetectable level to 6.3 × 10(5) cells/L. Superheating A. castellanii at 75-95 °C for 20 min revealed significant reductions in both EMA-qPCR and qPCR detectable Acanthamoeba target sequences with an adverse association between heating temperature and qPCR-determined DNA quantity (r = -0.76 to -0.93, p < 0.0001). Moreover, A. castellanii trophozoites were more sensitive to superheat stress than the cells being encysted for 6 and 13 d (p < 0.05). This is the first study to quantify environmental Acanthamoeba and characterize their responses to superheating by EMA-qPCR. The quantitative data provided in this study facilitate to understand better the relative risk for human exposed to viable Acanthamoeba and the efficacy of superheating against Acanthamoeba.
Collapse
Affiliation(s)
- Ching-Wen Chang
- Institute of Environmental Health, College of Public Health, National Taiwan University, Taipei, 100, Taiwan, Republic of China,
| | | | | | | |
Collapse
|
12
|
De Cooman L, Flahou B, Houf K, Smet A, Ducatelle R, Pasmans F, Haesebrouck F. Survival of Helicobacter suis bacteria in retail pig meat. Int J Food Microbiol 2013; 166:164-7. [PMID: 23880243 DOI: 10.1016/j.ijfoodmicro.2013.05.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/08/2013] [Accepted: 05/24/2013] [Indexed: 12/12/2022]
Abstract
Helicobacter (H.) suis colonizes the gastric mucosa of pigs world-wide and is the most prevalent non-Helicobacter pylori Helicobacter species in humans. This agent might be transmitted to humans by manipulation or consumption of contaminated pork. H. suis is a very fastidious micro-organism and is extremely difficult to isolate. Therefore, we developed a non-culture dependent, quantitative detection method allowing differentiation of viable from dead H. suis bacteria in pork. This was established by a combination of ethidium bromide monoazide (EMA) treatment and real-time (RT)-PCR. This EMA RT-PCR was applied to 50 retail pork samples. In two samples, viable H. suis bacteria were detected. Sequence analysis of the obtained PCR products confirmed the presence of H. suis DNA. Viable H. suis bacteria persisted for at least 48h in experimentally contaminated pork. In conclusion, consumption of contaminated pork may constitute a new route of transmission for H. suis infections in humans.
Collapse
Affiliation(s)
- Lien De Cooman
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium.
| | | | | | | | | | | | | |
Collapse
|
13
|
Sánchez MC, Marín MJ, Figuero E, Llama-Palacios A, León R, Blanc V, Herrera D, Sanz M. Quantitative real-time PCR combined with propidium monoazide for the selective quantification of viable periodontal pathogens in an in vitro
subgingival biofilm model. J Periodontal Res 2013; 49:20-8. [DOI: 10.1111/jre.12073] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2013] [Indexed: 12/01/2022]
Affiliation(s)
- M. C. Sánchez
- Research Laboratory; Faculty of Dentistry, Complutense University of Madrid; Spain
| | - M. J. Marín
- Research Laboratory; Faculty of Dentistry, Complutense University of Madrid; Spain
| | - E. Figuero
- Research Laboratory; Faculty of Dentistry, Complutense University of Madrid; Spain
| | - A. Llama-Palacios
- Research Laboratory; Faculty of Dentistry, Complutense University of Madrid; Spain
| | | | | | - D. Herrera
- Etiology and Therapy of Periodontal Disease Research Group, Faculty of Dentistry, Complutense University of Madrid; Spain
| | - M. Sanz
- Etiology and Therapy of Periodontal Disease Research Group, Faculty of Dentistry, Complutense University of Madrid; Spain
| |
Collapse
|
14
|
Abstract
High-throughput pyrosequencing and quantitative PCR (Q-PCR) analysis offer greatly improved accuracy and depth of characterisation of lower respiratory infections. However, such approaches suffer from an inability to distinguish between DNA derived from viable and non-viable bacteria. This discrimination represents an important step in characterising microbial communities, particularly in contexts with poor clearance of material or high antimicrobial stress, as non-viable bacteria and extracellular DNA can contribute significantly to analyses. Pre-treatment of samples with propidium monoazide (PMA) is an effective approach to non-viable cell exclusion (NVCE). However, the impact of NVCE on microbial community characteristics (abundance, diversity, composition and structure) is not known. Here, adult cystic fibrosis (CF) sputum samples were used as a paradigm. The effects of PMA treatment on CF sputum bacterial community characteristics, as analysed by pyrosequencing and enumeration by species-specific (Pseudomonas aeruginosa) and total bacterial Q-PCR, were assessed. At the local community level, abundances of both total bacteria and of P. aeruginosa were significantly lower in PMA-treated sample portions. Meta-analysis indicated no overall significant differences in diversity; however, PMA treatment resulted in a significant alteration in local community membership in all cases. In contrast, at the metacommunity level, PMA treatment resulted in an increase in community evenness, driven by an increase in diversity, predominately representing rare community members. Importantly, PMA treatment facilitated the detection of both recognised and emerging CF pathogens, significantly influencing 'core' and 'satellite' taxa group membership. Our findings suggest failure to implement NVCE may result in skewed bacterial community analyses.
Collapse
|
15
|
Agustí G, Fittipaldi M, Morató J, Codony F. Viable quantitative PCR for assessing the response of Candida albicans to antifungal treatment. Appl Microbiol Biotechnol 2012; 97:341-9. [DOI: 10.1007/s00253-012-4524-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 10/15/2012] [Accepted: 10/19/2012] [Indexed: 11/28/2022]
|
16
|
Progress in understanding preferential detection of live cells using viability dyes in combination with DNA amplification. J Microbiol Methods 2012; 91:276-89. [DOI: 10.1016/j.mimet.2012.08.007] [Citation(s) in RCA: 270] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/16/2012] [Accepted: 08/16/2012] [Indexed: 11/20/2022]
|
17
|
Sánchez MC, Marín MJ, Figuero E, Llama-Palacios A, Herrera D, Sanz M. Analysis of viable vs. dead Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis using selective quantitative real-time PCR with propidium monoazide. J Periodontal Res 2012; 48:213-20. [PMID: 22957816 DOI: 10.1111/j.1600-0765.2012.01522.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2012] [Indexed: 11/26/2022]
Abstract
BACKGROUND AND OBJECTIVES One of the major disadvantages of DNA-based microbial diagnostics is their inability to differentiate DNA between viable and dead microorganisms, which could be important when studying etiologically relevant pathogens. The aim of this investigation was to optimize a method for the selective detection and quantification of only viable Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis cells by combining quantitative real-time polymerase chain reaction (qPCR) and propidium monoazide (PMA). MATERIAL AND METHODS Three different concentrations of PMA (10, 50 or 100 μm) were added to suspensions of 10(6) (CFU)/mL of viable/dead A. actinomycetemcomitans and P. gingivalis cells. After DNA isolation, qPCR was carried out using specific primers and probes for the tested bacteria. PMA was further tested with different mixtures containing varying ratios of viable and dead cells. The efficacy of PMA to detect viable/dead cells was tested by analysis of variance. RESULTS For these specific bacterial pathogens, 100 μm PMA resulted in a significant reduction of qPCR amplification with dead cells (10(6) CFU/mL), while with viable cells no significant inhibition was detected. PMA was also effective in detecting selectively viable cells by qPCR detection, when mixtures of varying ratios of viable and dead bacteria were used. CONCLUSIONS This study demonstrated the efficiency of PMA for differentiating viable and dead A. actinomycetemcomitans and P. gingivalis cells. This method of PMA-qPCR may be useful for monitoring new antimicrobial strategies and for assessing the pathogenic potential of A. actinomycetemcomitans and P. gingivalis in different oral conditions when using molecular diagnostic methods.
Collapse
Affiliation(s)
- M C Sánchez
- ETEP (Aetiology and Therapy of Periodontal Diseases) Research Group, University Complutense of Madrid, Madrid, Spain
| | | | | | | | | | | |
Collapse
|