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Aralar A, Goshia T, Ramchandar N, Lawrence SM, Karmakar A, Sharma A, Sinha M, Pride DT, Kuo P, Lecrone K, Chiu M, Mestan KK, Sajti E, Vanderpool M, Lazar S, Crabtree M, Tesfai Y, Fraley SI. Universal Digital High-Resolution Melt Analysis for the Diagnosis of Bacteremia. J Mol Diagn 2024; 26:349-363. [PMID: 38395408 PMCID: PMC11090205 DOI: 10.1016/j.jmoldx.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/04/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Fast and accurate diagnosis of bloodstream infection is necessary to inform treatment decisions for septic patients, who face hourly increases in mortality risk. Blood culture remains the gold standard test but typically requires approximately 15 hours to detect the presence of a pathogen. We, therefore, assessed the potential for universal digital high-resolution melt (U-dHRM) analysis to accomplish faster broad-based bacterial detection, load quantification, and species-level identification directly from whole blood. Analytical validation studies demonstrated strong agreement between U-dHRM load measurement and quantitative blood culture, indicating that U-dHRM detection is highly specific to intact organisms. In a pilot clinical study of 17 whole blood samples from pediatric patients undergoing simultaneous blood culture testing, U-dHRM achieved 100% concordance when compared with blood culture and 88% concordance when compared with clinical adjudication. Moreover, U-dHRM identified the causative pathogen to the species level in all cases where the organism was represented in the melt curve database. These results were achieved with a 1-mL sample input and sample-to-answer time of 6 hours. Overall, this pilot study suggests that U-dHRM may be a promising method to address the challenges of quickly and accurately diagnosing a bloodstream infection.
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Affiliation(s)
- April Aralar
- Department of Bioengineering, University of California, San Diego, La Jolla, California
| | - Tyler Goshia
- Department of Bioengineering, University of California, San Diego, La Jolla, California
| | - Nanda Ramchandar
- Department of Pediatrics, Naval Medical Center San Diego, San Diego, California; Division of Infectious Diseases, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Shelley M Lawrence
- Division of Neonatology, Department of Pediatrics, The University of Utah, Salt Lake City, Utah
| | | | | | | | - David T Pride
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Peiting Kuo
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Khrissa Lecrone
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Megan Chiu
- Department of Pathology, University of California, San Diego, La Jolla, California
| | - Karen K Mestan
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Eniko Sajti
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Michelle Vanderpool
- Department of Pathology and Laboratory Medicine, Rady Children's Hospital-San Diego, San Diego, California
| | - Sarah Lazar
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Melanie Crabtree
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Yordanos Tesfai
- Division of Neonatology, Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Stephanie I Fraley
- Department of Bioengineering, University of California, San Diego, La Jolla, California.
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Li S, Liu X, Li Z, Liu H, Hu D. Combination of direct boiling and glass beads increases the purity and accuracy of bacterial DNA extraction. Biotechnol J 2023; 18:e2300135. [PMID: 37464951 DOI: 10.1002/biot.202300135] [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: 03/27/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/20/2023]
Abstract
Extraction of DNA is a key step in molecular biology experiments and important for counting tiny microbial individuals. Direct boiling and mechanical cell lysis like glass beads are two independent physical extraction methods, thus crossing the barriers of thresholds of magnitude in popular reagent kits or traditional spread plate method when non-equilibrium phenomenon is ongoing. The two approaches above were combined to generate a new one. In three typical microbial species, direct boiling with glass beads significantly increased the purity of DNA solution compared with some other methods (p < 0.05). The qPCR results of them were closer to direct microscopy counting than some other methods. Therefore, it provides a new choice in extracting bacterial DNA for specific circumstances.
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Affiliation(s)
- Shuaishuai Li
- School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- Institute of Environmental Biology and Life Support Technology, Beihang University, Beijing, China
| | - Xiaolei Liu
- School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- Institute of Environmental Biology and Life Support Technology, Beihang University, Beijing, China
| | - Ziye Li
- School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- Institute of Environmental Biology and Life Support Technology, Beihang University, Beijing, China
| | - Hong Liu
- School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- Institute of Environmental Biology and Life Support Technology, Beihang University, Beijing, China
- International Joint Research Center of Aerospace Biotechnology and Medical Engineering, Beijing, China
- State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, China
| | - Dawei Hu
- School of Biological Science and Medical Engineering, Beihang University, Beijing, China
- Institute of Environmental Biology and Life Support Technology, Beihang University, Beijing, China
- International Joint Research Center of Aerospace Biotechnology and Medical Engineering, Beijing, China
- State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, China
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Aralar A, Goshia T, Ramchandar N, Lawrence SM, Karmakar A, Sharma A, Sinha M, Pride DT, Kuo P, Lecrone K, Chiu M, Mestan K, Sajti E, Vanderpool M, Lazar S, Crabtree M, Tesfai Y, Fraley SI. Universal digital high resolution melt analysis for the diagnosis of bacteremia. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.07.23295215. [PMID: 37732245 PMCID: PMC10508820 DOI: 10.1101/2023.09.07.23295215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Fast and accurate diagnosis of bloodstream infection is necessary to inform treatment decisions for septic patients, who face hourly increases in mortality risk. Blood culture remains the gold standard test but typically requires ∼15 hours to detect the presence of a pathogen. Here, we assess the potential for universal digital high-resolution melt (U-dHRM) analysis to accomplish faster broad-based bacterial detection, load quantification, and species-level identification directly from whole blood. Analytical validation studies demonstrated strong agreement between U-dHRM load measurement and quantitative blood culture, indicating that U-dHRM detection is highly specific to intact organisms. In a pilot clinical study of 21 whole blood samples from pediatric patients undergoing simultaneous blood culture testing, U-dHRM achieved 100% concordance when compared with blood culture and 90.5% concordance when compared with clinical adjudication. Moreover, U-dHRM identified the causative pathogen to the species level in all cases where the organism was represented in the melt curve database. These results were achieved with a 1 mL sample input and sample-to-answer time of 6 hrs. Overall, this pilot study suggests that U-dHRM may be a promising method to address the challenges of quickly and accurately diagnosing a bloodstream infection. Universal digital high resolution melt analysis for the diagnosis of bacteremia April Aralar, Tyler Goshia, Nanda Ramchandar, Shelley M. Lawrence, Aparajita Karmakar, Ankit Sharma, Mridu Sinha, David Pride, Peiting Kuo, Khrissa Lecrone, Megan Chiu, Karen Mestan, Eniko Sajti, Michelle Vanderpool, Sarah Lazar, Melanie Crabtree, Yordanos Tesfai, Stephanie I. Fraley.
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Nye AK, Rogovskyy A, Lazarus MA, Amore R, Mankin KMT. Effectiveness of chlorhexidine diacetate and povidone-iodine in antiseptic preparation of the canine external ear canal prior to total ear canal ablation with bulla osteotomy procedure: A preliminary study. Vet Med Sci 2023; 9:1998-2005. [PMID: 37418348 PMCID: PMC10508515 DOI: 10.1002/vms3.1200] [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: 02/11/2023] [Revised: 05/04/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
OBJECTIVE This article is a preliminary study to compare the ability of 0.05% chlorhexidine diacetate (CD) and 1% povidone-iodine (PI) solutions to reduce bacterial contamination on the canine external ear canal during initial patient preparation and comparison of the incidence of immediate tissue reactions. STUDY DESIGN The study is a multi-institutional, randomised, clinical prospective study. ANIMALS OR SAMPLE POPULATION Dogs (n = 19) undergoing total ear canal ablation with bulla osteotomy (TECABO). METHODS The external ear of each dog was cleaned with the assigned antiseptic solution. Culture of the ear was performed by standard techniques to semi-quantitatively evaluate bacterial growth and to identify bacterial organisms pre- and post-antiseptic use. RESULTS Both antiseptic groups showed a significant reduction in bacterial growth score (BGS) between pre- and post-antiseptic use (CD p = 0.009, PI p = 0.005). There was no difference in the reduction of BGS between CD and PI solutions (p = 0.53). Minor adverse skin reactions occurred in 25% of cases. There was no significant difference in the occurrence of adverse skin reactions between antiseptics (p = 0.63). CONCLUSION CD and PI were similarly able to decrease the number of bacteria on the external ear following initial preparation. No difference in the incidence of adverse tissue reactions was found. CLINICAL SIGNIFICANCE Properly diluted aqueous formulations of either antiseptic may be used for safe preparation limited to the external ear canal of dogs. Additional studies evaluating outcomes such as duration of bacterial inhibition and incidence of surgical site infections are needed to fully elucidate differences between CD and PI antiseptics prior to TECABO.
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Affiliation(s)
- Alicia K. Nye
- Department of Small Animal Clinical SciencesCollege of Veterinary Medicine and Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | - Artem Rogovskyy
- Department of Veterinary PathobiologyCollege of Veterinary Medicine and Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
| | | | - Riley Amore
- Dallas Veterinary Surgical CenterDallasTexasUSA
| | - Kelley M. Thieman Mankin
- Department of Small Animal Clinical SciencesCollege of Veterinary Medicine and Biomedical Sciences, Texas A&M UniversityCollege StationTexasUSA
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Jo TS. Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis. Proc Biol Sci 2023; 290:20230979. [PMID: 37253423 PMCID: PMC10229230 DOI: 10.1098/rspb.2023.0979] [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: 05/01/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial and aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to the detection of aged eDNA that has long since been released from the individual and is more likely to be detected at a site further away from its source. In order to address the issue, this manuscript focuses on the state of eDNA, proposing new methodologies to estimate the age of eDNA: (1) DNA damage rate, (2) eDNA particle size distribution, and (3) viable cell-derived eDNA. In addition, the manuscript also focuses on the shorter persistence of environmental RNA (eRNA) compared with eDNA, highlighting the application of eRNA and environmental nucleic acid ratio for assessing the age of the genetic materials in water. Although substantial further research is essential to support the feasibility of these methodologies, incorporating time-scale information into eDNA analysis would update current eDNA analysis, improve the accuracy and reliability of eDNA-based monitoring, and further refine eDNA analysis as a useful monitoring tool in ecology, fisheries and various environmental sciences.
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Affiliation(s)
- Toshiaki S. Jo
- Research Fellow of Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
- Ryukoku Center for Biodiversity Science, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga 520-2194, Japan
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-cho, Seta, Otsu City, Shiga 520-2194, Japan
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Zaccaria E, Klaassen T, Alleleyn AM, Boekhorst J, Chervaux C, Smokvina T, Troost FJ, Kleerebezem M. L. rhamnosus CNCM I-3690 survival, adaptation, and small bowel microbiome impact in human. Gut Microbes 2023; 15:2244720. [PMID: 37589280 PMCID: PMC10438856 DOI: 10.1080/19490976.2023.2244720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/05/2023] [Accepted: 08/01/2023] [Indexed: 08/18/2023] Open
Abstract
Fermented foods and beverages are a significant source of dietary bacteria that enter the gastrointestinal (GI) tract. However, little is known about how these microbes survive and adapt to the small intestinal environment. Colony-forming units (CFU) enumeration and viability qPCR of Lacticaseibacillus rhamnosus CNCM I-3690 in the ileal effluent of 10 ileostomy subjects during 12-h post consumption of a dairy product fermented with this strain demonstrated the high level of survival of this strain during human small intestine passage. Metatranscriptome analyses revealed the in situ transcriptome of L. rhamnosus in the small intestine, which was contrasted with transcriptome data obtained from in vitro cultivation. These comparative analyses revealed substantial metabolic adaptations of L. rhamnosus during small intestine transit, including adjustments of carbohydrate metabolism, surface-protein expression, and translation machinery. The prominent presence of L. rhamnosus in the effluent samples did not elicit an appreciable effect on the composition of the endogenous small intestine microbiome, but significantly altered the ecosystem's overall activity profile, particularly of pathways associated with carbohydrate metabolism. Strikingly, two of the previously recognized gut-brain metabolic modules expressed in situ by L. rhamnosus (inositol degradation and glutamate synthesis II) are among the most dominantly enriched activities in the ecosystem's activity profile. This study establishes the survival capacity of L. rhamnosus in the human small intestine and highlights its functional adjustment in situ, which we postulate to play a role in the probiotic effects associated with this strain.
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Affiliation(s)
- Edoardo Zaccaria
- Host Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Tim Klaassen
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, The Netherlands
- Food Innovation and Health, Department of Human Biology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Venlo, The Netherlands
| | - Annick M.E. Alleleyn
- Food Innovation and Health, Department of Human Biology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Venlo, The Netherlands
| | - Jos Boekhorst
- Host Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Tamara Smokvina
- Danone Nutricia Research, Centre Daniel Carasso, Palaiseau, France
| | - Freddy J. Troost
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Michiel Kleerebezem
- Host Microbe Interactomics Group, Wageningen University & Research, Wageningen, The Netherlands
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Li YH, Zeng J, Wang Z, Wang TY, Wu SY, Zhu XY, Zhang X, Shan BH, Gao CZ, Wang SH, Wu FG. Sulfur-Doped Organosilica Nanodots as a Universal Sensor for Ultrafast Live/Dead Cell Discrimination. BIOSENSORS 2022; 12:1000. [PMID: 36354509 PMCID: PMC9688158 DOI: 10.3390/bios12111000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Rapid and accurate differentiation between live and dead cells is highly desirable for the evaluation of cell viability. Here, we report the application of the orange-emitting sulfur-doped organosilica nanodots (S-OSiNDs) for ultrafast (30 s), ultrasensitive (1 μg/mL), and universal staining of the dead bacterial, fungal, and mammalian cells but not the live ones, which satisfies the requirements of a fluorescent probe that can specifically stain the dead cells. We further verify that the fluorescence distribution range of S-OSiNDs (which are distributed in cytoplasm and nucleus) is much larger than that of the commercial dead/fixed cell/tissue staining dye RedDot2 (which is distributed in the nucleus) in terms of dead mammalian cell staining, indicating that S-OSiNDs possess a better staining effect of dead cells than RedDot2. Overall, S-OSiNDs can be used as a robust fluorescent probe for ultrafast and accurate discrimination between dead and live cells at a single cell level, which may find a variety of applications in the biomedical field.
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Kiefer A, Byrd PM, Tang P, Jones G, Galles K, Fallico V, Wong C. Viability droplet digital polymerase chain reaction accurately enumerates probiotics and provides insight into damage experienced during storage. Front Microbiol 2022; 13:966264. [PMID: 36386724 PMCID: PMC9648155 DOI: 10.3389/fmicb.2022.966264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/26/2022] [Indexed: 12/05/2022] Open
Abstract
Probiotics are typically enumerated by agar plate counting (PC) techniques. PC has several limitations including poor specificity, high variability, inability to enumerate dead cells, viable but non-culturable cells and cells in complex matrices. Viability droplet digital polymerase chain reaction (v-ddPCR) is an emerging enumeration technique with improved specificity, precision, and the ability to enumerate cells in varying states of culturability or in complex matrices. Good correlation and agreement between v-ddPCR and PC is well documented, but not much research has been published on the comparison when enumerating freeze-dried (FD) probiotics during storage. In this study, v-ddPCR utilizing PE51 (PE51-ddPCR), a combination of propidium monoazide (PMA) and ethidium monoazide (EMA), was evaluated as alternative enumeration technique to PC on blends of four FD probiotic strains over the course of a 3-month storage study with accelerated conditions. When PMA and EMA are combined (PE51), this study demonstrates agreement (bias = 7.63e+9, LOA = 4.38e+10 to 5.9e+10) and association (r = 0.762) between PC and v-ddPCR, at or above levels of an accepted alternative method. Additionally, v-ddPCR with individual dyes PMA and EMA provide insight into how they individually contribute to the viable counts obtained by PE51-ddPCR and provide a more specific physiological understanding of how probiotics cope with or experience damage during storage.
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Point-of-Care Lateral Flow Detection of Viable Escherichia coli O157:H7 Using an Improved Propidium Monoazide-Recombinase Polymerase Amplification Method. Foods 2022; 11:3207. [PMCID: PMC9602316 DOI: 10.3390/foods11203207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The detection of both viable and viable but non-culturable (VBNC) Escherichia coli O157:H7 is a crucial part of food safety. Traditional culture-dependent methods are lengthy, expensive, laborious, and unable to detect VBNC. Hence, there is a need to develop a rapid, simple, and cost-effective detection method to differentiate between viable/dead E. coli O157:H7 and detect VBNC cells. In this work, recombinase polymerase amplification (RPA) was developed for the detection of viable E. coli O157:H7 through integration with propidium monoazide (PMAxx). Initially, two primer sets, targeting two different genes (rfbE and stx) were selected, and DNA amplification by RPA combined with PMAxx treatment and the lateral flow assay (LFA) was carried out. Subsequently, the rfbE gene target was found to be more effective in inhibiting the amplification from dead cells and detecting only viable E. coli O157:H7. The assay’s detection limit was found to be 102 CFU/mL for VBNC E. coli O157:H7 when applied to spiked commercial beverages including milk, apple juice, and drinking water. pH values from 3 to 11 showed no significant effect on the efficacy of the assay. The PMAxx-RPA-LFA was completed at 39 °C within 40 min. This study introduces a rapid, robust, reliable, and reproducible method for detecting viable bacterial counts. In conclusion, the optimised assay has the potential to be used by the food and beverage industry in quality assurance related to E. coli O157:H7.
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Teker B, de Vries H, Heijman T, van Dam A, Schim van der Loeff M, Jongen VW. Spontaneous clearance of asymptomatic anogenital and pharyngeal Neisseria gonorrhoeae: a secondary analysis from the NABOGO trial. Sex Transm Infect 2022; 99:219-225. [PMID: 35820778 DOI: 10.1136/sextrans-2022-055488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/25/2022] [Indexed: 11/04/2022] Open
Abstract
INTRODUCTION Spontaneous clearance of asymptomatic Neisseria gonorrhoeae (NG) does occur, but data are scarce. We aimed to assess spontaneous clearance among patients with asymptomatic anal, pharyngeal, vaginal and urethral NG infections who participated in the New AntiBiotic treatment Options for uncomplicated GOnorrhoea (NABOGO) trial. In addition, we assessed the determinants associated with spontaneous clearance. METHODS The NABOGO trial (Trial registration number: NCT03294395) was a randomised controlled, double-blind, single-centre trial assessing non-inferiority of ertapenem, gentamicin and fosfomycin to ceftriaxone for treatment of uncomplicated gonorrhoea. For asymptomatic NABOGO participants, we collected pre-enrolment and enrolment visit samples before trial medication was given. Spontaneous clearance was defined as a positive pre-enrolment nucleic acid amplification test (NAAT) result, followed by a negative NAAT at enrolment. We compared the median time between pre-enrolment and enrolment visits for patients who cleared spontaneously and for those who did not. Determinants of spontaneous clearance were assessed using logistic regression. RESULTS Thirty-two of 221 (14.5%) anal NG infections cleared spontaneously, 17 of 91 (18.7%) pharyngeal, 3 of 13 (23.1%) vaginal and 9 of 28 (32.1%) urethral NG infections. The median time between the pre-enrolment and enrolment visit was longer for patients who cleared their pharyngeal infection spontaneously compared with those who did not (median 8 days (IQR=7-11) vs 6 days (IQR=4-8), p=0.012); no determinants of clearance at other sites were identified. Overall, patients with more days between the pre-enrolment and enrolment visit were more likely to clear spontaneously (adjusted OR=1.06 per additional day, 95% CI 1.01 to 1.12). No association between location of NG infection and spontaneous clearance was found. CONCLUSIONS A significant proportion of asymptomatic patients cleared their NG infections spontaneously. Given these results, treatment of all NG infections after a one-time NAAT may be excessive, and more research on the natural history of NG is needed to improve antibiotic stewardship.
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Affiliation(s)
- Buhari Teker
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Henry de Vries
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Department of Dermatology, Amsterdam institute for Infection and Immunity (AII), location Academic Medical Center, Amsterdam, the Netherlands
| | - Titia Heijman
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
| | - Alje van Dam
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Maarten Schim van der Loeff
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Internal Medicine, Amsterdam Institute for Infection Immunity (AII), Amsterdam, The Netherlands
| | - Vita Willemijn Jongen
- Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, The Netherlands
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11
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Yu XW, Liu X, Jiang YW, Li YH, Gao G, Zhu YX, Lin F, Wu FG. Rose Bengal-Derived Ultrabright Sulfur-Doped Carbon Dots for Fast Discrimination between Live and Dead Cells. Anal Chem 2022; 94:4243-4251. [PMID: 35235297 DOI: 10.1021/acs.analchem.1c04658] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The discrimination between dead and live cells is crucial for cell viability evaluation. Carbon dots (CDs), with advantages like simple and cost-effective synthesis, excellent biocompatibility, and high photostability, have shown potential for realizing selective live/dead cell staining. However, most of the developed CDs with the live/dead cell discrimination capacity usually have low photoluminescence quantum yields (PLQYs) and excitation wavelength-dependent fluorescence emission (which can cause fluorescence overlap with other fluorescent probes and make dual-color live/dead staining impossible), and hence, developing ultrabright CDs with excitation wavelength-independent fluorescence emission property for live/dead cell discrimination becomes an important task. Here, using a one-pot hydrothermal method, we prepared ultrasmall (∼1.6 nm), ultrabright (PLQY: ∼78%), and excitation wavelength-independent sulfur-doped carbon dots (termed S-CDs) using rose bengal and 1,4-dimercaptobenzene as raw materials and demonstrated that the S-CDs could rapidly (∼5 min) and accurately distinguish dead cells from live ones for almost all the cell types including bacterial, fungal, and animal cells in a wash-free manner. We confirmed that the S-CDs could rapidly pass through the dead cell surfaces to enter the interior of the dead cells, thus visualizing these dead cells. In contrast, the S-CDs could not enter the interior of live cells and thus could not stain these live cells. We further verified that the S-CDs presented better biocompatibility and higher photostability than the commercial live/dead staining dye propidium iodide, ensuring its bright application prospect in cell imaging and cell viability assessment. Overall, this work develops a type of CDs capable of realizing the live/dead cell discrimination of almost all the cell types (bacterial, fungal, and animal cells), which has seldom been achieved by other fluorescent nanoprobes.
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Affiliation(s)
- Xin-Wang Yu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing 210096, P. R. China
| | - Xiaoyang Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing 210096, P. R. China
| | - Yao-Wen Jiang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing 210096, P. R. China
| | - Yan-Hong Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing 210096, P. R. China
| | - Ge Gao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing 210096, P. R. China
| | - Ya-Xuan Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing 210096, P. R. China
| | - Fengming Lin
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing 210096, P. R. China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing 210096, P. R. China
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Alsante AN, Thornton DCO, Brooks SD. Ocean Aerobiology. Front Microbiol 2021; 12:764178. [PMID: 34777320 PMCID: PMC8586456 DOI: 10.3389/fmicb.2021.764178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022] Open
Abstract
Ocean aerobiology is defined here as the study of biological particles of marine origin, including living organisms, present in the atmosphere and their role in ecological, biogeochemical, and climate processes. Hundreds of trillions of microorganisms are exchanged between ocean and atmosphere daily. Within a few days, tropospheric transport potentially disperses microorganisms over continents and between oceans. There is a need to better identify and quantify marine aerobiota, characterize the time spans and distances of marine microorganisms’ atmospheric transport, and determine whether microorganisms acclimate to atmospheric conditions and remain viable, or even grow. Exploring the atmosphere as a microbial habitat is fundamental for understanding the consequences of dispersal and will expand our knowledge of biodiversity, biogeography, and ecosystem connectivity across different marine environments. Marine organic matter is chemically transformed in the atmosphere, including remineralization back to CO2. The magnitude of these transformations is insignificant in the context of the annual marine carbon cycle, but may be a significant sink for marine recalcitrant organic matter over long (∼104 years) timescales. In addition, organic matter in sea spray aerosol plays a significant role in the Earth’s radiative budget by scattering solar radiation, and indirectly by affecting cloud properties. Marine organic matter is generally a poor source of cloud condensation nuclei (CCN), but a significant source of ice nucleating particles (INPs), affecting the formation of mixed-phase and ice clouds. This review will show that marine biogenic aerosol plays an impactful, but poorly constrained, role in marine ecosystems, biogeochemical processes, and the Earth’s climate system. Further work is needed to characterize the connectivity and feedbacks between the atmosphere and ocean ecosystems in order to integrate this complexity into Earth System models, facilitating future climate and biogeochemical predictions.
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Affiliation(s)
- Alyssa N Alsante
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Daniel C O Thornton
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Sarah D Brooks
- Department of Atmospheric Sciences, Texas A&M University, College Station, TX, United States
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Adamson PC, Klausner JD. The staying power of pharyngeal gonorrhea: implications for public health and antimicrobial resistance. Clin Infect Dis 2021; 73:583-585. [PMID: 33508084 DOI: 10.1093/cid/ciab074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Indexed: 01/06/2023] Open
Affiliation(s)
- Paul C Adamson
- Division of Infectious Diseases, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Jeffrey D Klausner
- Division of Infectious Diseases, David Geffen School of Medicine, University of California, Los Angeles, CA.,Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA
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Munir MT, Pailhories H, Eveillard M, Irle M, Aviat F, Dubreil L, Federighi M, Belloncle C. Testing the Antimicrobial Characteristics of Wood Materials: A Review of Methods. Antibiotics (Basel) 2020; 9:E225. [PMID: 32370037 PMCID: PMC7277147 DOI: 10.3390/antibiotics9050225] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/27/2020] [Accepted: 04/27/2020] [Indexed: 01/08/2023] Open
Abstract
Some wood species have antimicrobial properties, making them a better choice over inert surfaces in certain circumstances. However, the organic and porous nature of wood raises questions regarding the use of this material in hygienically important places. Therefore, it is reasonable to investigate the microbial survival and the antimicrobial potential of wood via a variety of methods. Based on the available literature, this review classifies previously used methods into two broad categories: one category tests wood material by direct bacterial contact, and the other tests the action of molecules previously extracted from wood on bacteria and fungi. This article discusses the suitability of these methods to wood materials and exposes knowledge gaps that can be used to guide future research. This information is intended to help the researchers and field experts to select suitable methods for testing the hygienic safety and antimicrobial properties of wood materials.
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Affiliation(s)
- Muhammad Tanveer Munir
- Laboratoire Innovation Matériau Bois Habitat Apprentissage (LIMBHA), Ecole Supérieure du Bois, 7 rue Christian Pauc, 44306 Nantes, France; (M.T.M.); (M.I.)
| | - Hélène Pailhories
- Laboratoire HIFIH, UPRES EA3859, SFR 4208, Université d’Angers, 49933 Angers, France;
- Laboratoire de bactériologie, CHU Angers, 49933 Angers, France;
| | - Matthieu Eveillard
- Laboratoire de bactériologie, CHU Angers, 49933 Angers, France;
- CRCINA, Inserm, Université de Nantes and Université d’Angers, 44200 Nantes, France
| | - Mark Irle
- Laboratoire Innovation Matériau Bois Habitat Apprentissage (LIMBHA), Ecole Supérieure du Bois, 7 rue Christian Pauc, 44306 Nantes, France; (M.T.M.); (M.I.)
| | - Florence Aviat
- Your ResearcH-Bio-Scientific, 307 la Gauterie, 44430 Le Landreau, France;
| | - Laurence Dubreil
- PAnTher, Oniris, INRA, Université Bretagne Loire, F-44307 Nantes, France;
| | - Michel Federighi
- UMR INRA 1014 SECALIM, Oniris, route de Gachet, CS 40706, 44307 Nantes cedex 03, France;
| | - Christophe Belloncle
- Laboratoire Innovation Matériau Bois Habitat Apprentissage (LIMBHA), Ecole Supérieure du Bois, 7 rue Christian Pauc, 44306 Nantes, France; (M.T.M.); (M.I.)
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