1
|
Sterzenbach T, Neumann V, Trips E, Basche S, Hannig C, Kühne MT. Establishment of a Protocol for Viability qPCR in Dental Hard Tissues. Microorganisms 2024; 12:1400. [PMID: 39065168 PMCID: PMC11278712 DOI: 10.3390/microorganisms12071400] [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: 06/06/2024] [Revised: 06/25/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
The aim of the study was to establish a live/dead qPCR with propidium monoazide (PMA) that can quantitatively differentiate between viable/non-viable microorganisms in dental hard tissues. Human premolars (n = 88) were prepared with nickel-titanium instruments and incubated with E. faecalis (21 d). Subsequently, the bacteria in half of the teeth were devitalized by heat inactivation (100 °C, 2 h). The following parameters were tested: PMA concentrations at 0 µmol (control), 50 µmol, 100 µmol, and 200 µmol; PMA incubation times of 30 min and 60 min, and blue light treatment for 30 min and 60 min. The teeth were ground using a cryomill and the bacterial DNA was quantified using qPCR, ANOVA, and p = 0.05. The qPCR of the control group detected a similar number of avital 9.94 × 106 and vital 1.61 × 107 bacterial cells. The use of PMA inhibited the amplification of DNA from non-viable cells during qPCR. As a result, the best detection of avital bacteria was achieved with the following PMA parameters: (concentration, incubation time, blue light treatment) 200-30-30; 5.53 × 104 (avital) and 1.21 × 100.7 (vital). The live/dead qPCR method using PMA treatment is suitable for the differentiation and quantification of viable/non-viable microorganisms in dentin, as well as to evaluate the effectiveness of different preparation procedures and antimicrobial irrigants in other biological hard substances.
Collapse
Affiliation(s)
- Torsten Sterzenbach
- Policlinic of Operative Dentistry, Periodontology and Pediatric Dentistry, Medical Faculty Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany; (T.S.); (V.N.); (S.B.); (C.H.)
| | - Vanessa Neumann
- Policlinic of Operative Dentistry, Periodontology and Pediatric Dentistry, Medical Faculty Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany; (T.S.); (V.N.); (S.B.); (C.H.)
| | - Evelyn Trips
- Coordination Centre for Clinical Trials, Faculty of Medicine Carl Gustav Carus, Dresden University of Technology, Fetscherstraße 74, 01309 Dresden, Germany
| | - Sabine Basche
- Policlinic of Operative Dentistry, Periodontology and Pediatric Dentistry, Medical Faculty Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany; (T.S.); (V.N.); (S.B.); (C.H.)
| | - Christian Hannig
- Policlinic of Operative Dentistry, Periodontology and Pediatric Dentistry, Medical Faculty Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany; (T.S.); (V.N.); (S.B.); (C.H.)
| | - Marie-Theres Kühne
- Policlinic of Operative Dentistry, Periodontology and Pediatric Dentistry, Medical Faculty Carl Gustav Carus, Dresden University of Technology, 01307 Dresden, Germany; (T.S.); (V.N.); (S.B.); (C.H.)
| |
Collapse
|
2
|
Chai Z, Liu Y, Jia S, Li F, Hu Z, Deng Y, Yue C, Tang YZ. DNA and RNA Stability of Marine Microalgae in Cold-Stored Sediments and Its Implications in Metabarcoding Analyses. Int J Mol Sci 2024; 25:1724. [PMID: 38339002 PMCID: PMC10855355 DOI: 10.3390/ijms25031724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The ever-increasing applications of metabarcoding analyses for environmental samples demand a well-designed assessment of the stability of DNA and RNA contained in cells that are deposited or buried in marine sediments. We thus conducted a qPCR quantification of the DNA and RNA in the vegetative cells of three microalgae entrapped in facsimile marine sediments and found that >90% of DNA and up to 99% of RNA for all microalgal species were degraded within 60 days at 4 °C. A further examination of the potential interference of the relic DNA of the vegetative cells with resting cyst detection in sediments was performed via a metabarcoding analysis in artificial marine sediments spiked with the vegetative cells of two Kareniaceae dinoflagellates and the resting cysts of another three dinoflagellates. The results demonstrated a dramatic decrease in the relative abundances of the two Kareniaceae dinoflagellates in 120 days, while those of the three resting cysts increased dramatically. Together, our results suggest that a positive detection of microalgae via metabarcoding analysis in DNA or RNA extracted from marine sediments strongly indicates the presence of intact or viable cysts or spores due to the rapid decay of relic DNA/RNA. This study provides a solid basis for the data interpretation of metabarcoding surveys, particularly in resting cyst detection.
Collapse
Affiliation(s)
- Zhaoyang Chai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- Laoshan Laboratory, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yuyang Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- Laoshan Laboratory, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Siyang Jia
- Yellow Sea and East Sea Buoy Observation Station, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
| | - Fengting Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- Laoshan Laboratory, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- Laoshan Laboratory, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- Laoshan Laboratory, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Caixia Yue
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying-Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Z.C.); (Y.L.); (F.L.); (Z.H.); (Y.D.); (C.Y.)
- Laoshan Laboratory, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| |
Collapse
|
3
|
Boyle AG, O'Shea K, Stefanovski D, Rankin SC. Detection of Viable Streptococcus equi equi Using Propidium Monoazide Polymerase Chain Reaction. J Equine Vet Sci 2023; 128:104893. [PMID: 37481173 DOI: 10.1016/j.jevs.2023.104893] [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: 02/10/2023] [Revised: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 07/24/2023]
Abstract
There is debate around the clinical significance of Streptococcus equi subsp. equi detection in low numbers using quantitative real-time PCR (qPCR). Propidium monoazide (PMA) qPCR has been used to differentiate DNA from viable and nonviable bacterial cells. The aim of this study was to evaluate the ability of PMA eqbE SEQ2190 triplex qPCR to differentiate DNA from viable and nonviable S. equi in positive and suspect positive clinical specimens. Fifty-seven stored (frozen and refrigerated) positive (36) or suspect positive (21) clinical specimens (determined via SeeI qPCR as the gold standard) were tested using eqbE SEQ2190 triplex qPCR with (+) and without (-) PMA pretreatment. Cycle thresholds were higher when using PMA indicating a mixture of heat killed and viable cells. Number of S. equi positive specimens were as follows: 6/57 eqbE + PMA, 13/57 eqbE -PMA (Chi- squared 3.1, p = .079); 10/57 SEQ2190 +PMA, 53/57 SEQ2190 -PMA (Chi- squared 65.6, p < .0001). The mean cycle thresholds were as follows: 23.88 eqbE -PMA, 29.89 eqbE + PMA (p = .04); 24.9 SEQ2190 -PMA, 31.9 SEQ2190 +PMA (p < .0001). PMA qPCR can be used to determine S. equi viability, but testing should be performed on fresh specimens.
Collapse
Affiliation(s)
- Ashley G Boyle
- Department of Clinical Studies New Bolton Center, University of Pennsylvania School of Veterinary Medicine, Kennett Square, PA.
| | - Kathleen O'Shea
- Department of Clinical Studies New Bolton Center, University of Pennsylvania School of Veterinary Medicine, Kennett Square, PA; Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA
| | - Darko Stefanovski
- Department of Clinical Studies New Bolton Center, University of Pennsylvania School of Veterinary Medicine, Kennett Square, PA
| | - Shelley C Rankin
- Department of Pathobiology, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA
| |
Collapse
|
4
|
Cunha AP, Henriques R, Cardoso S, Freitas PP, Carvalho CM. Rapid and multiplex detection of nosocomial pathogens on a phage-based magnetoresistive lab-on-chip platform. Biotechnol Bioeng 2021; 118:3164-3174. [PMID: 34037981 DOI: 10.1002/bit.27841] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/06/2021] [Accepted: 05/16/2021] [Indexed: 11/11/2022]
Abstract
Nosocomial or hospital-acquired infections (HAIs) have a major impact on mortality worldwide. Enterococcus and Staphylococcus are among the leading causes of HAIs and thus are important pathogens to control mainly due to their increased antibiotic resistance. The gold-standard diagnostic methods for HAIs are time-consuming, which hinders timely and adequate treatment. Therefore, the development of fast and accurate diagnostic tools is an urgent demand. In this study, we combined the sensitivity of magnetoresistive (MR) sensors, the portability of a lab-on-chip platform, and the specificity of phage receptor binding proteins (RBPs) as probes for the rapid and multiplex detection of Enterococcus and Staphylococcus. For this, bacterial cells were firstly labelled with magnetic nanoparticles (MNPs) functionalized with RBPs and then measured on the MR sensors. The results indicate that the RBP-MNPS provided a specific individual and simultaneous capture of more than 70% of Enterococcus and Staphylococcus cells. Moreover, high signals from the MR sensors were obtained for these samples, providing the detection of both pathogens at low concentrations (10 CFU/ml) in less than 2 h. Overall, the lab-on-chip MR platform herein presented holds great potential to be used as a point-of-care for the rapid, sensitive and specific multiplex diagnosis of bacterial infections.
Collapse
Affiliation(s)
- Alexandra P Cunha
- International Iberian Nanotechnology Laboratory (INL), Braga, Portugal.,Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
| | - Raquel Henriques
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - Susana Cardoso
- Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - Paulo P Freitas
- International Iberian Nanotechnology Laboratory (INL), Braga, Portugal.,Instituto de Engenharia de Sistemas e Computadores - Microsistemas e Nanotecnologias (INESC MN) and IN - Institute of Nanoscience and Nanotechnology, Lisbon, Portugal
| | - Carla M Carvalho
- International Iberian Nanotechnology Laboratory (INL), Braga, Portugal
| |
Collapse
|
5
|
Clinical and Molecular Microbiological Evaluation of Regenerative Endodontic Procedures in Immature Permanent Teeth. J Endod 2020; 46:1448-1454. [DOI: 10.1016/j.joen.2020.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/17/2020] [Accepted: 07/04/2020] [Indexed: 11/17/2022]
|
6
|
Elverson TR, Kontz BJ, Markell SG, Harveson RM, Mathew FM. Quantitative PCR Assays Developed for Diaporthe helianthi and Diaporthe gulyae for Phomopsis Stem Canker Diagnosis and Germplasm Screening in Sunflower ( Helianthus annuus). PLANT DISEASE 2020; 104:793-800. [PMID: 31951508 DOI: 10.1094/pdis-09-19-1827-re] [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] [Indexed: 06/10/2023]
Abstract
Phomopsis stem canker of sunflower is caused by two fungal pathogens, Diaporthe helianthi and Diaporthe gulyae, in the United States. In this study, two quantitative PCR (qPCR) assays were developed to detect and quantify D. helianthi and D. gulyae in sunflower. The two assays differentiated the two fungi from each other, other species of the genus Diaporthe, and pathogens, and they have high efficiency (>90%). The qPCR assays detected the two pathogens on plant samples exhibiting Phomopsis stem canker symptoms sampled from commercial sunflower fields in Minnesota, Nebraska, North Dakota, and South Dakota. Furthermore, the assays were used to screen cultivated sunflower accessions for resistance to D. helianthi and D. gulyae. The disease severity index (DSI) of the accessions significantly correlated (P < 0.0001) with the amount of pathogen DNA from the qPCR assays. The qPCR assays identified PI664232 and PI561918 to be significantly less susceptible (P ≤ 0.05) to D. helianthi and D. gulyae, respectively, when compared with the susceptible check cultivar HA 288, and this was in agreement with the DSI. These results suggest that the qPCR assays for D. helianthi and D. gulyae can be used as a reliable tool to diagnose Phomopsis stem canker and screen sunflower germplasm for disease resistance.
Collapse
Affiliation(s)
- Taylor R Elverson
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57007
| | - Brian J Kontz
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57007
| | - Samuel G Markell
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102
| | - Robert M Harveson
- Department of Plant Pathology, University of Nebraska-Lincoln, Scottsbluff, NE 69361
| | - Febina M Mathew
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57007
| |
Collapse
|
7
|
Prado LC, Gavini G, Silveira ADC, Nakamura VC, Mayer MPA, Pinheiro ET. Comparison of rRNA-based reverse transcription PCR and rDNA-based PCR for the detection of streptococci in root canal infections. J Appl Oral Sci 2019; 27:e20180256. [PMID: 31365706 PMCID: PMC6690712 DOI: 10.1590/1678-7757-2018-0256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 02/26/2019] [Indexed: 11/21/2022] Open
Abstract
Objective The rDNA-based method is unable to distinguish between alive and dead cells. Alternatively, bacterial viability can be assessed by molecular methods based on ribosomal RNA (rRNA). Therefore, this study aimed to detect viable streptococci in root canal samples using rRNA-based reverse transcription polymerase chain reaction (RT-PCR), compared to an rDNA-based PCR assay. Methodology Microbiological root canal samples were obtained from 32 teeth with primary endodontic infections before (S1) and after chemomechanical preparation (S2), and after removal of intracanal medication (S3). RNA and DNA were extracted, and complementary DNA (cDNA) was synthesized from RNA using RT reaction. cDNA and genomic DNA were subjected to PCR with primers complementary to the 16S rRNA sequences of Streptococcus spp. McNemar’s test was used to compare the detection rate of both assays (P<0.05). Results Streptococci were detected in 28.12% (9/32) and 37.5% (12/32) of S1 samples using rRNA- and rDNA-based PCR assays, respectively. In contrast, they were detected in only 6.25% (2/32) of S2 samples using rRNA-based RT-PCR, compared to 15.62% (5/32) using rDNA-based PCR. Finally, in S3 samples, streptococci were not detected by rRNA, whereas rDNA-based PCR still detected the bacteria in 12.5% (4/32) of the samples. The total number of PCR-positive reactions in the rDNA-based PCR was higher than in the rRNA-based assay (P<0.05). Conclusions The rRNA-based RT-PCR showed a lower detection rate of streptococci when compared to the rDNA-based PCR, suggesting that the latter may have detected dead cells of streptococci in root canal samples.
Collapse
Affiliation(s)
- Laís Cunha Prado
- Universidade de São Paulo, Faculdade de Odontologia, São Paulo, SP, Brasil
| | - Giulio Gavini
- Universidade de São Paulo, Faculdade de Odontologia, São Paulo, SP, Brasil
| | | | | | - Marcia Pinto Alves Mayer
- Universidade de São Paulo, Faculdade de Odontologia, Instituto de Ciências Biomédicas, São Paulo, SP, Brasil
| | | |
Collapse
|
8
|
Abdullah AS, Turo C, Moffat CS, Lopez-Ruiz FJ, Gibberd MR, Hamblin J, Zerihun A. Real-Time PCR for Diagnosing and Quantifying Co-infection by Two Globally Distributed Fungal Pathogens of Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1086. [PMID: 30140271 PMCID: PMC6095046 DOI: 10.3389/fpls.2018.01086] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/05/2018] [Indexed: 06/01/2023]
Abstract
Co-infections - invasions of a host-plant by multiple pathogen species or strains - are common, and are thought to have consequences for pathogen ecology and evolution. Despite their apparent significance, co-infections have received limited attention; in part due to lack of suitable quantitative tools for monitoring of co-infecting pathogens. Here, we report on a duplex real-time PCR assay that simultaneously distinguishes and quantifies co-infections by two globally important fungal pathogens of wheat: Pyrenophora tritici-repentis and Parastagonospora nodorum. These fungi share common characteristics and host species, creating a challenge for conventional disease diagnosis and subsequent management strategies. The assay uses uniquely assigned fluorogenic probes to quantify fungal biomass as nucleic acid equivalents. The probes provide highly specific target quantification with accurate discrimination against non-target closely related fungal species and host genes. Quantification of the fungal targets is linear over a wide range (5000-0.5 pg DNA μl-1) with high reproducibility (RSD ≤ 10%). In the presence of host DNA in the assay matrix, fungal biomass can be quantified up to a fungal to wheat DNA ratio of 1 to 200. The utility of the method was demonstrated using field samples of a cultivar sensitive to both pathogens. While visual and culture diagnosis suggested the presence of only one of the pathogen species, the assay revealed not only presence of both co-infecting pathogens (hence enabling asymptomatic detection) but also allowed quantification of relative abundances of the pathogens as a function of disease severity. Thus, the assay provides for accurate diagnosis; it is suitable for high-throughput screening of co-infections in epidemiological studies, and for exploring pathogen-pathogen interactions and dynamics, none of which would be possible with conventional approaches.
Collapse
Affiliation(s)
- Araz S. Abdullah
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Chala Turo
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Caroline S. Moffat
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Francisco J. Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Mark R. Gibberd
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - John Hamblin
- Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - Ayalsew Zerihun
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| |
Collapse
|
9
|
Lee S, Bae S. Evaluating the newly developed dye, DyeTox13 Green C-2 Azide, and comparing it with existing EMA and PMA for the differentiation of viable and nonviable bacteria. J Microbiol Methods 2018; 148:33-39. [DOI: 10.1016/j.mimet.2018.03.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/10/2018] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
|
10
|
Da Collina GA, Tempestini-Horliana ACR, da Silva DDFT, Longo PL, Makabe MLF, Pavani C. Oral hygiene in intensive care unit patients with photodynamic therapy: study protocol for randomised controlled trial. Trials 2017; 18:385. [PMID: 28830529 PMCID: PMC5568342 DOI: 10.1186/s13063-017-2133-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/03/2017] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND In intensive care units (ICUs), nosocomial infections are prevalent conditions and they have been related to high mortality indexes. Some studies have suggested that inefficient oral hygiene and ventilator-associated pneumonia (VAP) are related. Nowadays, in the Brazilian public health system there is no well-defined protocol for oral hygiene in an ICU. Due to the drawbacks of the use of antibiotics, photodynamic therapy (PDT) has emerged as an interesting technique in order to reduce antimicrobial-resistant pathogens. Methylene blue (MB) is the most common chemical agent for PDT in Brazil. However, new formulations for improved effectiveness are still lacking. The objective of this study is to evaluate the use of an MB mouthwash as an effective oral-hygiene procedure in an ICU and to show that oral hygiene using PDT with MB mouthwash may reduce VAP frequency to rates similar to, or higher than, chlorhexidine. METHODS Phase 1 will evaluate the most effective cleaning procedure, while phase 2 will correlate oral hygiene to VAP incidence. At the start of phase 1, the ICU patients will be randomly allocated into three different groups (10 patients/group): the efficacy of chlorhexidine, classical MB-PDT, and mouthwash MB-PDT will all be measured for the quantification of viable bacteria, both pre- and post-treatment, by a Reverse Transcription Polymerase Chain Reaction (RT-PCR). In phase 2, the most effective procedure found in phase 1 and a mechanical cleaning with filtered water will be carried out daily, once a day, over 5 days, with a total of 52 ICU patients randomly allocated into the two groups. The clinical records will be evaluated in order to find any pneumonic diagnoses. DISCUSSION Since a variety of bacterial species are related to VAP, a universal primer for bacteria will be used in order to quantify the total bacteria count in the participants' samples. In order to quantify only the living bacteria before DNA extraction, the samples will be treated with propidium monoazide. This will infiltrate the dead bacteria and will intercalate the DNA bases, avoiding their DNA amplification. This will be the first trial to evaluate MB-PDT in a mouthwash formula that can increase the effectiveness due to the control of MB aggregation. The results of this study will be able to generate an easy and low-cost protocol to be used in an ICU for the Brazilian public health system. TRIAL REGISTRATION This protocol was approved by the Research Ethics Committee of the Conjunto Hospitalar do Mandaqui (1.317.834, CAAE: 49273515.9.3001.5551) and it was registered in Registro Brasileiro de Ensaios Clínicos (ReBEC number: RBR-94bvrc;). First received: 12 July 2015; 1st version 6 June 2016. Data will be published in a peer-reviewed journal.
Collapse
Affiliation(s)
- Gabriela Alves Da Collina
- Biophotonics Applied to Health Sciences Postgraduation Program, Universidade Nove de Julho – UNINOVE, R. Vergueiro, 235/249, CEP 01504-001 São Paulo, Brazil
| | - Anna Carolina Ratto Tempestini-Horliana
- Biophotonics Applied to Health Sciences Postgraduation Program, Universidade Nove de Julho – UNINOVE, R. Vergueiro, 235/249, CEP 01504-001 São Paulo, Brazil
| | - Daniela de Fátima Teixeira da Silva
- Biophotonics Applied to Health Sciences Postgraduation Program, Universidade Nove de Julho – UNINOVE, R. Vergueiro, 235/249, CEP 01504-001 São Paulo, Brazil
| | - Priscila Larcher Longo
- Biophotonics Applied to Health Sciences Postgraduation Program, Universidade Nove de Julho – UNINOVE, R. Vergueiro, 235/249, CEP 01504-001 São Paulo, Brazil
| | | | - Christiane Pavani
- Biophotonics Applied to Health Sciences Postgraduation Program, Universidade Nove de Julho – UNINOVE, R. Vergueiro, 235/249, CEP 01504-001 São Paulo, Brazil
| |
Collapse
|
11
|
Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nat Microbiol 2016; 2:16242. [PMID: 27991881 DOI: 10.1038/nmicrobiol.2016.242] [Citation(s) in RCA: 407] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/20/2016] [Indexed: 12/27/2022]
Abstract
Extracellular DNA from dead microorganisms can persist in soil for weeks to years1-3. Although it is implicitly assumed that the microbial DNA recovered from soil predominantly represents intact cells, it is unclear how extracellular DNA affects molecular analyses of microbial diversity. We examined a wide range of soils using viability PCR based on the photoreactive DNA-intercalating dye propidium monoazide4. We found that, on average, 40% of both prokaryotic and fungal DNA was extracellular or from cells that were no longer intact. Extracellular DNA inflated the observed prokaryotic and fungal richness by up to 55% and caused significant misestimation of taxon relative abundances, including the relative abundances of taxa integral to key ecosystem processes. Extracellular DNA was not found in measurable amounts in all soils; it was more likely to be present in soils with low exchangeable base cation concentrations, and the effect of its removal on microbial community structure was more profound in high-pH soils. Together, these findings imply that this 'relic DNA' remaining in soil after cell death can obscure treatment effects, spatiotemporal patterns and relationships between microbial taxa and environmental conditions.
Collapse
|