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Elhassan E, Omolo CA, Gafar MA, Kiruri LW, Ibrahim UH, Ismail EA, Devnarain N, Govender T. Disease-Inspired Design of Biomimetic Tannic Acid-Based Hybrid Nanocarriers for Enhancing the Treatment of Bacterial-Induced Sepsis. Mol Pharm 2024. [PMID: 39214595 DOI: 10.1021/acs.molpharmaceut.4c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
This study explored the development of novel biomimetic tannic acid-based hybrid nanocarriers (HNs) for targeted delivery of ciprofloxacin (CIP-loaded TAH-NPs) against bacterial-induced sepsis. The prepared CIP-loaded TAH-NPs exhibited appropriate physicochemical characteristics and demonstrated biocompatibility and nonhemolytic properties. Computational simulations and microscale thermophoresis studies validated the strong binding affinity of tannic acid (TA) and its nanoformulation to human Toll-like receptor 4, surpassing that of the natural substrate lipopolysaccharide (LPS), suggesting a potential competitive inhibition against LPS-induced inflammatory responses. CIP released from TAH-NPs displayed a sustained release profile over 72 h. The in vitro antibacterial activity studies revealed that CIP-loaded TAH-NPs exhibited enhanced antibacterial efficacy and efflux pump inhibitory activity. Specifically, they showed a 3-fold increase in biofilm eradication activity against MRSA and a 2-fold increase against P. aeruginosa compared to bare CIP. Time-killing assays demonstrated complete bacterial clearance within 8 h of treatment with CIP-loaded TAH-NPs. In vitro DPPH scavenging and anti-inflammatory investigations confirmed the ability of the prepared hybrid nanosystem to neutralize reactive oxygen species (ROS) and modulate LPS-induced inflammatory responses. Collectively, these results suggest that CIP-loaded TAH-NPs may serve as an innovative nanocarrier for the effective and targeted delivery of antibiotics against bacterial-induced sepsis.
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Affiliation(s)
- Eman Elhassan
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag Durban X54001, South Africa
| | - Calvin A Omolo
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag Durban X54001, South Africa
- Department of Pharmaceutics and Pharmacy Practice, School of Pharmacy and Health Sciences, United States International University-Africa, P.O. Box 14634-00800, Nairobi 00800, Kenya
| | - Mohammed Ali Gafar
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag Durban X54001, South Africa
- Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum 11111, Sudan
| | - Lucy W Kiruri
- Department of Chemistry, Kenyatta University, P.O. Box 43844, Nairobi 00100, Kenya
| | - Usri H Ibrahim
- Discipline of Human Physiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4300, South Africa
| | - Eman A Ismail
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag Durban X54001, South Africa
| | - Nikita Devnarain
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag Durban X54001, South Africa
| | - Thirumala Govender
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag Durban X54001, South Africa
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Choi S, Piri A, Jung J, An S, Hwang J. Determination of airborne influenza virus and coronavirus infectivity using capsid integrity polymerase chain reaction. JOURNAL OF HAZARDOUS MATERIALS 2024; 479:135544. [PMID: 39216245 DOI: 10.1016/j.jhazmat.2024.135544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Accurate airborne virus monitoring is important for preventing the spread of infectious diseases. Although standard reverse transcription-quantitative polymerase chain reaction (RT-qPCR) can efficiently detect viral ribonucleic acid (RNA), it cannot determine whether the RNA is associated with active (infectious) or inactive (non-infectious) viruses. Plaque assay is the gold standard for determining viral infectivity but is laborious and time-consuming. This study explored the viral infectivity of H1N1 influenza virus and human coronavirus (HCoV-229E) using capsid integrity RT-qPCR, where virus samples were pretreated with reagents penetrating viruses with damaged capsids, impeding amplification by binding to their RNA. Therefore, the amplified signals corresponded solely to active viruses with undamaged capsids. Propidium monoazide (PMA) and platinum (IV) chloride (PtCl4) were used to investigate the effects of reagent concentration. Feasibility tests revealed that PtCl4 was more efficient than PMA, with optimal concentrations of 125-250 μM and 250-500 μM for H1N1 influenza virus and HCoV-229E, respectively. The results of percentage of active virus showed that capsid integrity RT-qPCR provided a trend similar to that of plaque assay, indicating an accurate measure of viral infectivity. Virus sampling in the laboratory and field highlighted the precision of this methodology for determining viral infectivity. Therefore, this methodology enables rapid and accurate detection of infectious airborne H1N1 influenza virus and HCoV-229E, allowing swift response to outbreaks.
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Affiliation(s)
- Sangsoo Choi
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Amin Piri
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea; Institute of Engineering Research, Yonsei University, Seoul 03722, Republic of Korea.
| | - Jiwoo Jung
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Sanggwon An
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jungho Hwang
- Department of Mechanical Engineering, Yonsei University, Seoul 03722, Republic of Korea.
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Li L, Bae S. Quantitative detection and survival analysis of VBNC Salmonella Typhimurium in flour using droplet digital PCR and DNA-intercalating dyes. Microbiol Spectr 2024; 12:e0024924. [PMID: 38975767 PMCID: PMC11302299 DOI: 10.1128/spectrum.00249-24] [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: 01/25/2024] [Accepted: 05/13/2024] [Indexed: 07/09/2024] Open
Abstract
The difficulty in detecting viable but non-culturable (VBNC) Salmonella by culture-dependent methods poses a risk to food safety. In our study, we applied a viability test to Salmonella following a lethal treatment and to flour samples inoculated with Salmonella to evaluate the effectiveness of viability polymerase chain reaction (PCR). Our findings revealed that the combination of both ddPCR and qPCR with those DNA-intercalating dyes could quantify viable cells at low concentrations when the plate counting method failed to detect them post-inactivation. Prolonged UV exposure did not induce cell membrane disruption, as confirmed with PMA-ddPCR, with insignificant differences in gene copies. However, samples exposed to DyeTox13 and DyeTox13 + EMA showed lower gene copy numbers, implying that enzymatic activity was decreased by UV exposure duration. In addition, temperature-dependent survival in flour revealed uniform decay rates and D values (time required for a 1 log reduction) of DNA in untreated samples across various temperatures. By contrast, different decay rates were observed with DNA-intercalating dyes (DyeTox13 and DyeTox13 + EMA), showing faster metabolic activity loss at higher temperatures in flour. The decay rates and D values, determined through plate counting and those DNA-intercalating dyes, indicated the potential presence of VBNC Salmonella. A strong correlation between DyeTox13 dyes and the plate counting method suggested DyeTox13 as a rapid alternative for detecting Salmonella in flour. The ddPCR with DNA-intercalating dyes could effectively evaluate Salmonella viability, facilitating more precise monitoring of VBNC in food. IMPORTANCE Salmonella, a major foodborne pathogen, poses significant risks, particularly to vulnerable groups like infants, older people, and the immunocompromised. Accurate detection is vital for public health and food safety, given its potential to cause severe and life-threatening symptoms. Our study demonstrated digital polymerase chain reaction (ddPCR) with DNA-intercalating dyes for identifying the different physiological statuses of Salmonella. Also, the application of ddPCR with DNA-intercalating dyes offers quantification of viable cells post-disinfection as an alternative method in food. Utilizing ddPCR and DNA-intercalating dyes, we enhanced the detection of VBNC Salmonella, a form often undetectable by conventional methods. This innovative approach could significantly improve the precision and efficiency of detection for viable Salmonella. By providing deeper insights into its transmission potential, our method is a critical tool in preventing outbreaks and ensuring the safety of food products. This research contributes substantially to global efforts in controlling foodborne illnesses and safeguarding public health.
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Affiliation(s)
- Liyan Li
- Department of Civil and Environmental Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Sungwoo Bae
- Department of Civil and Environmental Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
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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.
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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.)
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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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Lee SY, Oh SW. Point-of-Care Diagnostic System for Viable Salmonella Species via Improved Propidium Monoazide and Recombinase Polymerase Amplification Based Nucleic Acid Lateral Flow. Diagnostics (Basel) 2024; 14:831. [PMID: 38667476 PMCID: PMC11049151 DOI: 10.3390/diagnostics14080831] [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: 03/15/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Salmonella species are prominent foodborne microbial pathogens transmitted through contaminated food or water and pose a significant threat to human health. Accurate and rapid point-of-care (POC) diagnosis is gaining attention in effectively preventing outbreaks of foodborne disease. However, the presence of dead bacteria can interfere with an accurate diagnosis, necessitating the development of methods for the rapid, simple, and efficient detection of viable bacteria only. Herein, we used an improved propidium monoazide (PMAxx) to develop a nucleic acid lateral flow (NALF) assay based on recombinase polymerase amplification (RPA) to differentiate viable Salmonella Typhimurium. We selected an RPA primer set targeting the invA gene and designed a probe for NALF. RPA-based NALF was optimized for temperature (30-43 °C), time (1-25 min), and endonuclease IV concentration (0.025-0.15 unit/µL). PMAxx successfully eliminated false-positive results from dead S. Typhimurium, enabling the accurate detection of viable S. Typhimurium with a detection limit of 1.11 × 102 CFU/mL in pure culture. The developed method was evaluated with spiked raw chicken breast and milk with analysis completed within 25 min at 39 °C. This study has potential as a tool for the POC diagnostics of viable foodborne pathogens with high specificity, sensitivity, rapidity, and cost-effectiveness.
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Affiliation(s)
| | - Se-Wook Oh
- Department of Food and Nutrition, Kookmin University, Seoul 136-702, Republic of Korea;
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7
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Dorn-In S, Daldrup E, Mang S, Esteban-Cuesta I, Gareis M, Schwaiger K. Viable Campylobacter jejuni on Eggshells and Its Potential to Cross-contaminate Egg White and Yolk When Using a Manual Separation Technique, Determined by Culture and Propidium Monoazide (PMA) qPCR. J Food Prot 2024; 87:100246. [PMID: 38369191 DOI: 10.1016/j.jfp.2024.100246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 01/07/2024] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Manual separation of egg yolk from egg white using the eggshell is common practice in private households. For this, the egg is cracked and both components are separated by passing the egg yolk back and forth between the two halves of the eggshell, allowing the egg white to drip down while the egg yolk remains in the shell. During this process, the egg content naturally gets in contact with the outside of the eggshell, which might lead to a cross-contamination with its microorganisms, thus was correspondingly assessed in this study. Campylobacter jejuni is one of the most important zoonotic pathogens that can be found on eggshells. Therefore, this bacterium was used to artificially contaminate the eggshells (n = 22) with concentrations of 3.1 ± 0.6 log10 cfu/g. After separating the egg yolk from the egg white, cross-contamination was determined using culture and qPCR. Altogether, cross-contaminations with C. jejuni were found in 15 egg white (68%) and in three egg yolk (14%) samples. Afterward, 90 eggs from 30 egg packs from different producers in and around Munich (Germany) were obtained for field study purposes. To address the problem of culturing due to a possible viable but nonculturable (VBNC) status of C. jejuni, a method to differentiate viable and dead C. jejuni on eggshell using 10 µM propidium monoazide (PMA) and qPCR was developed. As a result, seven egg packs (23%) were positive for C. jejuni. Of these, only one (3%) was contaminated with viable cells, but still in a concentration of 3.3 log10 cells/g shell. According to these results and considering that eggshells might also be naturally contaminated with other pathogens, the authors recommend avoiding the manual separation technique of egg white and yolk by the eggshell. Especially if raw egg white or yolk is used for preparation of not sufficiently heated foods, where contaminating pathogens are not inactivated during processing, this technique might be a safety hazard for the consumer.
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Affiliation(s)
- Samart Dorn-In
- Unit of Food Hygiene and Technology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria.
| | - Eva Daldrup
- Chair of Food Safety and Analytics, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Schoenleutnerstr. 8, 85764 Oberschleissheim, Germany
| | - Sirkka Mang
- Chair of Food Safety and Analytics, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Schoenleutnerstr. 8, 85764 Oberschleissheim, Germany
| | - Irene Esteban-Cuesta
- Chair of Food Safety and Analytics, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Schoenleutnerstr. 8, 85764 Oberschleissheim, Germany
| | - Manfred Gareis
- Chair of Food Safety and Analytics, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Schoenleutnerstr. 8, 85764 Oberschleissheim, Germany
| | - Karin Schwaiger
- Unit of Food Hygiene and Technology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Veterinaerplatz 1, 1210 Vienna, Austria
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Krohn C, Jansriphibul K, Dias DA, Rees CA, Akker BVD, Boer JC, Plebanski M, Surapaneni A, O'Carroll D, Richard S, Batstone DJ, Ball AS. Dead in the water - Role of relic DNA and primer choice for targeted sequencing surveys of anaerobic sewage sludge intended for biological monitoring. WATER RESEARCH 2024; 253:121354. [PMID: 38428359 DOI: 10.1016/j.watres.2024.121354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/03/2024]
Abstract
DNA-based monitoring of microbial communities that are responsible for the performance of anaerobic digestion of sewage wastes has the potential to improve resource recoveries for wastewater treatment facilities. By treating sludge with propidium monoazide (PMA) prior to amplicon sequencing, this study explored how the presence of DNA from dead microbial biomass carried over with feed sludge may mislead process-relevant biomarkers, and whether primer choice impacts such assessments. Four common primers were selected for amplicon preparation, also to determine if universal primers have sufficient taxonomic or functional coverage for monitoring ecological performance; or whether two domain-specific primers for Bacteria and Archaea are necessary. Anaerobic sludges of three municipal continuously stirred-tank reactors in Victoria, Australia, were sampled at one time-point. A total of 240 amplicon libraries were sequenced on a Miseq using two universal and two domain-specific primer pairs. Untargeted metabolomics was chosen to complement biological interpretation of amplicon gene-based functional predictions. Diversity, taxonomy, phylogeny and functional potentials were systematically assessed using PICRUSt2, which can predict community wide pathway abundance. The two chosen universal primers provided similar diversity profiles of abundant Bacteria and Archaea, compared to the domain-specific primers. About 16 % of all detected prokaryotic genera covering 30 % of total abundances and 6 % of PICRUSt2-estimated pathway abundances were affected by PMA. This showed that dead biomass in the anaerobic digesters impacted DNA-based assessments, with implications for predicting active processes, such as methanogenesis, denitrification or the identification of organisms associated with biological foams. Hence, instead of running two sequencing runs with two different domain-specific primers, we propose conducting PMA-seq with universal primer pairs for routine performance monitoring. However, dead sludge biomass may have some predictive value. In principal component analysis the compositional variation of 239 sludge metabolites resembled that of 'dead-plus-alive' biomass, suggesting that dead organisms contributed to the potentially process-relevant sludge metabolome.
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Affiliation(s)
- Christian Krohn
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia.
| | - Kraiwut Jansriphibul
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia
| | - Daniel A Dias
- Centre for Advanced Sensory Science (CASS) Food Research Centre, School of Exercise and Nutrition Sciences, Deakin University, Melbourne Burwood Campus, 221 Burwood Highway, Burwood, Victoria 3125, Australia
| | - Catherine A Rees
- Melbourne Water Corporation, 990 La Trobe Street, Docklands, Victoria 3008, Australia
| | - Ben van den Akker
- South Australian Water Corporation, Adelaide, South Australia 5000, Australia
| | - Jennifer C Boer
- Cancer Aging and Vaccine Laboratory, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
| | - Magdalena Plebanski
- Cancer Aging and Vaccine Laboratory, School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria 3083, Australia
| | - Aravind Surapaneni
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia; South East Water, 101 Wells Street, Frankston, Victoria 3199, Australia
| | - Denis O'Carroll
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Stuetz Richard
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Damien J Batstone
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia; Australian Centre for Water and Environmental Biotechnology (ACWEB), Gehrmann Building, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andrew S Ball
- ARC Training Centre for the Transformation of Australia's Biosolids Resource, RMIT University, Building 215, Level 3, Room 003-06, RMIT Bundoora West Campus, 225-245 Plenty Road, Bundoora, Victoria 3083, Australia
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Dhar BC, Delgado Santander R, Aćimović SG. Improved Canker Processing and Viability Droplet Digital PCR Allow Detection of Erwinia amylovora Viable Nonculturable Cells in Apple Bark. Microorganisms 2024; 12:376. [PMID: 38399780 PMCID: PMC10893025 DOI: 10.3390/microorganisms12020376] [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: 11/19/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The bacterium Erwinia amylovora causes fire blight and continues to threaten global commercial apple and pear production. Conventional microbiology techniques cannot accurately determine the presence of live pathogen cells in fire blight cankers. Several factors may prevent E. amylovora from growing on solid culture media, including competing microbiota and the release of bacterial-growth-inhibitory compounds by plant material during sample processing. We previously developed a canker processing methodology and a chip-based viability digital PCR (v-dPCR) assay using propidium monoazide (PMA) to bypass these obstacles. However, sample analysis was still time-consuming and physically demanding. In this work, we improved the previous protocol using an automatic tissue homogenizer and transferred the chip-based v-dPCR to the BioRad QX200 droplet dPCR (ddPCR) platform. The improved sample processing method allowed the simultaneous, fast, and effortless processing of up to six samples. Moreover, the transferred v-ddPCR protocol was compatible with the same PMA treatment and showed a similar dynamic range, from 7.2 × 102 to 7.6 × 107 cells mL-1, as the previous v-dPCR. Finally, the improved protocol allowed, for the first time, the detection of E. amylovora viable but nonculturable (VBNC) cells in cankers and bark tissues surrounding cankers. Our v-ddPCR assay will enable new ways to evaluate resistant pome fruit tree germplasm, further dissect the E. amylovora life cycle, and elucidate E. amylovora physiology, epidemiology, and new options for canker management.
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Affiliation(s)
- Bidhan Chandra Dhar
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, 595 Laurel Grove Rd, Winchester, VA 22602, USA;
| | - Ricardo Delgado Santander
- Irrigated Agriculture Research and Extension Center, College of Agricultural, Human and Natural Resource Sciences, Washington State University, Prosser, WA 99350, USA;
| | - Srđan G. Aćimović
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, 595 Laurel Grove Rd, Winchester, VA 22602, USA;
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10
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Marole TA, Sibanda T, Buys EM. Assessing probiotic viability in mixed species yogurt using a novel propidium monoazide (PMAxx)-quantitative PCR method. Front Microbiol 2024; 15:1325268. [PMID: 38389538 PMCID: PMC10882272 DOI: 10.3389/fmicb.2024.1325268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Viability is a prerequisite for any therapeutic benefits associated with the ingestion of probiotic bacteria. Current culture-based techniques are inadequate for the enumeration of probiotics in mixed-species food products. This study utilized a quantitative PCR (qPCR) method coupled with propidium monoazide (PMAxx), and novel species-specific tuf gene primers to selectively enumerate Lacticaseibacillus rhamnosus, Bifidobacterium spp., and yogurt starter cultures in mixed-species probiotic yogurt. The method was optimized for PMAxx concentration and specificity and evaluated for efficiency and applicability. PMAxx-qPCR showed high specificity to the target organisms in mixed-species yogurt, quantifying only viable cells. The linear dynamic ranges were established over five to seven orders of magnitude. The assay was reliable with an efficiency of 91-99%, R2 values > 0.99, and a good correlation to the plate count method (r = 0.882). The results of this study demonstrate the high selectivity, improved lead time, and reliability of PMAxx-qPCR over the culture-dependent method, making it a valuable tool for inline viability verification during processing and improving probiotic quality assurance for processors and consumers.
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Affiliation(s)
- Tlaleo A Marole
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
| | - Thulani Sibanda
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
| | - Elna M Buys
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
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11
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Sibanda T, Marole TA, Thomashoff UL, Thantsha MS, Buys EM. Bifidobacterium species viability in dairy-based probiotic foods: challenges and innovative approaches for accurate viability determination and monitoring of probiotic functionality. Front Microbiol 2024; 15:1327010. [PMID: 38371928 PMCID: PMC10869629 DOI: 10.3389/fmicb.2024.1327010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024] Open
Abstract
Bifidobacterium species are essential members of a healthy human gut microbiota. Their presence in the gut is associated with numerous health outcomes such as protection against gastrointestinal tract infections, inflammation, and metabolic diseases. Regular intake of Bifidobacterium in foods is a sustainable way of maintaining the health benefits associated with its use as a probiotic. Owing to their global acceptance, fermented dairy products (particularly yogurt) are considered the ideal probiotic carrier foods. As envisioned in the definition of probiotics as "live organisms," the therapeutic functionalities of Bifidobacterium spp. depend on maintaining their viability in the foods up to the point of consumption. However, sustaining Bifidobacterium spp. viability during the manufacture and shelf-life of fermented dairy products remains challenging. Hence, this paper discusses the significance of viability as a prerequisite for Bifidobacterium spp. probiotic functionality. The paper focuses on the stress factors that influence Bifidobacterium spp. viability during the manufacture and shelf life of yogurt as an archetypical fermented dairy product that is widely accepted as a delivery vehicle for probiotics. It further expounds the Bifidobacterium spp. physiological and genetic stress response mechanisms as well as the methods for viability retention in yogurt, such as microencapsulation, use of oxygen scavenging lactic acid bacterial strains, and stress-protective agents. The report also explores the topic of viability determination as a critical factor in probiotic quality assurance, wherein, the limitations of culture-based enumeration methods, the challenges of species and strain resolution in the presence of lactic acid bacterial starter and probiotic species are discussed. Finally, new developments and potential applications of next-generation viability determination methods such as flow cytometry, propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR), next-generation sequencing, and single-cell Raman spectroscopy (SCRS) methods are examined.
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Affiliation(s)
- Thulani Sibanda
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
- Department of Biology, National of University of Lesotho, Maseru, Lesotho
| | - Tlaleo Azael Marole
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Mapitsi S. Thantsha
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Elna M. Buys
- Department of Consumer and Food Sciences, University of Pretoria, Pretoria, South Africa
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12
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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.
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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
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13
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Kevill JL, Farkas K, Ridding N, Woodhall N, Malham SK, Jones DL. Use of Capsid Integrity-qPCR for Detecting Viral Capsid Integrity in Wastewater. Viruses 2023; 16:40. [PMID: 38257740 PMCID: PMC10819219 DOI: 10.3390/v16010040] [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: 11/20/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Quantifying viruses in wastewater via RT-qPCR provides total genomic data but does not indicate the virus capsid integrity or the potential risk for human infection. Assessing virus capsid integrity in sewage is important for wastewater-based surveillance, since discharged effluent may pose a public health hazard. While integrity assays using cell cultures can provide this information, they require specialised laboratories and expertise. One solution to overcome this limitation is the use of photo-reactive monoazide dyes (e.g., propidium monoazide [PMAxx]) in a capsid integrity-RT-qPCR assay (ci-RT-qPCR). In this study, we tested the efficiency of PMAxx dye at 50 μM and 100 μM concentrations on live and heat-inactivated model viruses commonly detected in wastewater, including adenovirus (AdV), hepatitis A (HAV), influenza A virus (IAV), and norovirus GI (NoV GI). The 100 μM PMAxx dye concentration effectively differentiated live from heat-inactivated viruses for all targets in buffer solution. This method was then applied to wastewater samples (n = 19) for the detection of encapsulated AdV, enterovirus (EV), HAV, IAV, influenza B virus (IBV), NoV GI, NoV GII, and SARS-CoV-2. Samples were negative for AdV, HAV, IAV, and IBV but positive for EV, NoV GI, NoV GII, and SARS-CoV-2. In the PMAxx-treated samples, EV, NoV GI, and NoV GII showed -0.52-1.15, 0.9-1.51, and 0.31-1.69 log reductions in capsid integrity, indicating a high degree of potentially infectious virus in wastewater. In contrast, SARS-CoV-2 was only detected using RT-qPCR but not after PMAxx treatment, indicating the absence of encapsulated and potentially infectious virus. In conclusion, this study demonstrates the utility of PMAxx dyes to evaluate capsid integrity across a diverse range of viruses commonly monitored in wastewater.
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Affiliation(s)
- Jessica L. Kevill
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; (K.F.); (N.R.); (N.W.); or (D.L.J.)
| | - Kata Farkas
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; (K.F.); (N.R.); (N.W.); or (D.L.J.)
| | - Nicola Ridding
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; (K.F.); (N.R.); (N.W.); or (D.L.J.)
| | - Nicholas Woodhall
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; (K.F.); (N.R.); (N.W.); or (D.L.J.)
| | - Shelagh K. Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK;
| | - Davey L. Jones
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; (K.F.); (N.R.); (N.W.); or (D.L.J.)
- Centre for Sustainable Farming Systems, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
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14
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Boyte ME, Benkowski A, Pane M, Shehata HR. Probiotic and postbiotic analytical methods: a perspective of available enumeration techniques. Front Microbiol 2023; 14:1304621. [PMID: 38192285 PMCID: PMC10773886 DOI: 10.3389/fmicb.2023.1304621] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024] Open
Abstract
Probiotics are the largest non-herbal/traditional dietary supplements category worldwide. To be effective, a probiotic strain must be delivered viable at an adequate dose proven to deliver a health benefit. The objective of this article is to provide an overview of the various technologies available for probiotic enumeration, including a general description of each technology, their advantages and limitations, and their potential for the future of the probiotics industry. The current "gold standard" for analytical quantification of probiotics in the probiotic industry is the Plate Count method (PC). PC measures the bacterial cell's ability to proliferate into detectable colonies, thus PC relies on cultivability as a measure of viability. Although viability has widely been measured by cultivability, there has been agreement that the definition of viability is not limited to cultivability. For example, bacterial cells may exist in a state known as viable but not culturable (VBNC) where the cells lose cultivability but can maintain some of the characteristics of viable cells as well as probiotic properties. This led to questioning the association between viability and cultivability and the accuracy of PC in enumerating all the viable cells in probiotic products. PC has always been an estimate of the number of viable cells and not a true cell count. Additionally, newer probiotic categories such as Next Generation Probiotics (NGPs) are difficult to culture in routine laboratories as NGPs are often strict anaerobes with extreme sensitivity to atmospheric oxygen. Thus, accurate quantification using culture-based techniques will be complicated. Another emerging category of biotics is postbiotics, which are inanimate microorganisms, also often referred to as tyndallized or heat-killed bacteria. Obviously, culture dependent methods are not suitable for these products, and alternative methods are needed for their quantification. Different methodologies provide a more complete picture of a heterogeneous bacterial population versus PC focusing exclusively on the eventual multiplication of the cells. Alternative culture-independent techniques including real-time PCR, digital PCR and flow cytometry are discussed. These methods can measure viability beyond cultivability (i.e., by measuring cellular enzymatic activity, membrane integrity or membrane potential), and depending on how they are designed they can achieve strain-specific enumeration.
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Affiliation(s)
- Marie-Eve Boyte
- NutraPharma Consulting Services Inc., Sainte-Anne-des-Plaines, QC, Canada
| | | | - Marco Pane
- Probiotical Research s.r.l., Novara, Italy
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15
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Guo J, Fan F, Wang W, Wan M, Li Y. Development of PMA-qPCR assay to accurately and reproducible quantify viable bacteria of Paenibacillus polymyxa. Lett Appl Microbiol 2023; 76:ovad127. [PMID: 37952090 DOI: 10.1093/lambio/ovad127] [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: 05/06/2023] [Revised: 10/04/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
Paenibacillus polymyxa is an important biocontrol bacterium. The combination of propidium monoazide (PMA) and quantitative polymerase chain reactionq (qPCR) has proven effective in quantifying live bacteria from various microorganisms. The objective was to create a PMA-qPCR assay to precisely and consistently measure the number of living bacteria of biocontrol P. polymyxa. The primers were designed for the spo0A gene of P. polymyxa HY96-2. The optimal conditions for treating the target strain with PMA were a PMA concentration of 15 μg/mL, an incubation time of 5 min, and an exposure time of 10 min. The PMA-qPCR method had a limit of quantification (LOQ) of 1.0 × 103 CFU/mL for measuring the amount of viable P. polymyxa bacteria. The PMA-qPCR method is more sensitive than the qPCR method in detecting viable bacteria in the mixtures of viable and dead bacteria. The accuracy and reproducibility of quantifying viable P. polymyxa bacteria using the PMA-qPCR method were higher compared to the plate count method.
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Affiliation(s)
- Jiacai Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Fei Fan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weiliang Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Minxi Wan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yuanguang Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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16
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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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17
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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.
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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
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18
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Wang J, Wei B, Chen Z, Chen Y, Liu S, Zhang B, Zhu B, Ye D. A rapid and reliable method for the determination of Lactiplantibacillus plantarum during wine fermentation based on PMA-CELL-qPCR. Front Microbiol 2023; 14:1154768. [PMID: 37529324 PMCID: PMC10389660 DOI: 10.3389/fmicb.2023.1154768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/26/2023] [Indexed: 08/03/2023] Open
Abstract
Real-time monitoring of microbial dynamics during fermentation is essential for wine quality control. This study developed a method that combines the fluorescent dye propidium monoazide (PMA) with CELL-qPCR, which can distinguish between dead and live microbes for Lactiplantibacillus plantarum. This method could detect the quantity of microbes efficiently and rapidly without DNA extraction during wine fermentation. The results showed that (1) the PMA-CELL-qPCR enumeration method developed for L. plantarum was optimized for PMA treatment concentration, PMA detection sensitivity and multiple conditions of sample pretreatment in wine environment, and the optimized method can accurately quantify 104-108 CFU/mL of the target strain (L. plantarum) in multiple matrices; (2) when the concentration of dead bacteria in the system is 104 times higher than the concentration of live bacteria, there is an error of 0.5-1 lg CFU/mL in the detection results. The optimized sample pretreatment method in wine can effectively reduce the inhibitory components in the qPCR reaction system; (3) the optimized PMA-CELL-qPCR method was used to monitor the dynamic changes of L. plantarum during the fermentation of Cabernet Sauvignon wine, and the results were consistent with the plate counting method. In conclusion, the live bacteria quantification method developed in this study for PMA-CELL-qPCR in L. plantarum wines is accurate in quantification and simple in operation, and can be used as a means to accurately monitor microbial dynamics in wine and other fruit wines.
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Affiliation(s)
- Jie Wang
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Bo Wei
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Zhuojun Chen
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Yixin Chen
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Songyu Liu
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Bolin Zhang
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Baoqing Zhu
- Beijing Key Laboratory of Forestry Food Processing and Safety, School of Biological Science and Technology, Beijing Forestry University, Beijing, China
| | - Dongqing Ye
- Guangxi Key Laboratory of Fruits and Vegetables Storage-Processing Technology, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China
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19
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Kennedy JP, Wood K, Pitino M, Mandadi K, Igwe DO, Shatters RG, Widmer TL, Niedz R, Heck M. A Perspective on Current Therapeutic Molecule Screening Methods Against ' Candidatus Liberibacter asiaticus', the Presumed Causative Agent of Citrus Huanglongbing. PHYTOPATHOLOGY 2023; 113:1171-1179. [PMID: 36750555 DOI: 10.1094/phyto-12-22-0455-per] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Huanglongbing (HLB), referred to as citrus greening disease, is a bacterial disease impacting citrus production worldwide and is fatal to young trees and mature trees of certain varieties. In some areas, the disease is devastating the citrus industry. A successful solution to HLB will be measured in economics: citrus growers need treatments that improve tree health, fruit production, and most importantly, economic yield. The profitability of citrus groves is the ultimate metric that truly matters when searching for solutions to HLB. Scientific approaches used in the laboratory, greenhouse, or field trials are critical to the discovery of those solutions and to estimate the likelihood of success of a treatment aimed at commercialization. Researchers and the citrus industry use a number of proxy evaluations of potential HLB solutions; understanding the strengths and limitations of each assay, as well as how best to compare different assays, is critical for decision-making to advance therapies into field trials and commercialization. This perspective aims to help the reader compare and understand the limitations of different proxy evaluation systems based on the treatment and evaluation under consideration. The researcher must determine the suitability of one or more of these metrics to identify treatments and predict the usefulness of these treatments in having an eventual impact on citrus production and HLB mitigation. As therapies advance to field trials in the next few years, a reevaluation of these metrics will be useful to guide future research efforts on strategies to mitigate HLB and vascular bacterial pathogens in other perennial crops.
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Affiliation(s)
- John Paul Kennedy
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Fort Pierce, FL 34945
| | | | | | - Kranthi Mandadi
- Department of Plant Pathology and Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco, TX 78596
- Texas A&M AgriLife Institute for Advancing Health Through Agriculture, Texas A&M AgriLife, College Station, TX 77843
| | - David O Igwe
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
| | - Robert G Shatters
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Fort Pierce, FL 34945
| | - Timothy L Widmer
- U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
| | - Randall Niedz
- U.S. Horticultural Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Fort Pierce, FL 34945
| | - Michelle Heck
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853
- Emerging Pests and Pathogens Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Ithaca, NY 14853
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20
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Di Salvo E, Panebianco F, Panebianco A, Ziino G. Quantitative Detection of Viable but Nonculturable Vibrio parahaemolyticus in Frozen Bivalve Molluscs. Foods 2023; 12:2373. [PMID: 37372584 DOI: 10.3390/foods12122373] [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: 05/12/2023] [Revised: 06/06/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
Vibrio parahaemolyticus is a foodborne pathogen diffusely distributed in the marine environment and often isolated from raw seafood belonging to different species, mostly shellfish. Ingestion of under- or uncooked seafood contaminated by V. parahaemolyticus can cause severe gastrointestinal symptoms in humans. Due to its ability to withstand low temperatures, Vibrio spp. could survive in frozen seafoods for long periods by entering the viable but nonculturable state (VBNC) and may constitute an unrecognized source of food contamination and infection. In the present study, seventy-seven frozen bivalve molluscs (35 mussels; 42 clams) were subjected to the detection and enumeration of viable V. parahaemolyticus using standard culture methods. VBNC forms were detected and quantified by applying an optimized protocol based on Propidium Monoazide (PMA) and Quantitative PCR (qPCR). All samples were negative for both the detection and enumeration of V. parahaemolyticus by the standard culture methods. VBNC forms were detected in 11.7% of the samples (9/77), with values ranging from 1.67 to 2.29 Log CFU/g. Only clam samples were positive for the detection of VBNC forms. The results of this study highlighted that VBNC V. parahaemolyticus may be present in frozen bivalve molluscs. Further data on the prevalence of VBNC V. parahaemolyticus in frozen seafood are needed in order to perform a robust risk assessment.
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Affiliation(s)
- Eleonora Di Salvo
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, Viale Palatucci snc, 98168 Messina, Italy
| | - Felice Panebianco
- Department of Veterinary Sciences, University of Turin, Largo Braccini 2, Grugliasco, 10095 Turin, Italy
| | - Antonio Panebianco
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, Viale Palatucci snc, 98168 Messina, Italy
| | - Graziella Ziino
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, Viale Palatucci snc, 98168 Messina, Italy
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Thilakarathna SH, Chui L. A Pilot Study to Detect Viable Salmonella spp. in Diarrheal Stool Using Viability Real-Time PCR as a Culture-Independent Diagnostic Tool in a Clinical Setting. Int J Mol Sci 2023; 24:9979. [PMID: 37373127 DOI: 10.3390/ijms24129979] [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: 05/15/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Frontline laboratories are adopting culture-independent diagnostic testing (CIDT) such as nucleic acid amplification tests (NAATs) due to numerous advantages over culture-based testing methods. Paradoxically, the viability of pathogens, a crucial factor determining active infections, cannot be confirmed with current NAATs alone. A recent development of viability PCR (vPCR) was introduced to mitigate this limitation associated with real-time PCR (qPCR) by using a DNA-intercalating dye to remove residual and dead cell DNA. This study assessed the applicability of the vPCR assay on diarrheal stools. Eighty-five diarrheal stools confirmed for Salmonellosis were tested via qPCR and vPCR using in-house primers and probe targeting the invA gene. vPCR-negative stools (Ct cut off > 31) were enriched in mannitol selenite broth (MSB) to verify low bacterial loads. vPCR assay showed ~89% sensitivity (qPCR- and vPCR-positive stools: 76/85). vPCR-negative stools (9/85; qPCR-positive: 5; qPCR-negative: 4) were qPCR- and culture-positive post-MSB-enrichment and confirmed the presence of low viable bacterial loads. Random sampling error, low bacterial loads, and receiving stools in batches could contribute to false negatives. This is a pilot study and further investigations are warranted to explore vPCR to assess pathogen viability in a clinical setting, especially when culture-based testing is unavailable.
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Affiliation(s)
- Surangi H Thilakarathna
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Alberta Precision Laboratories, Public Health Laboratory (ProvLab), Edmonton, AB T6G 2J2, Canada
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22
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Yang J, Xu H, Ke Z, Kan N, Zheng E, Qiu Y, Huang M. Absolute quantification of viable Vibrio cholerae in seawater samples using multiplex droplet digital PCR combined with propidium monoazide. Front Microbiol 2023; 14:1149981. [PMID: 37362935 PMCID: PMC10288211 DOI: 10.3389/fmicb.2023.1149981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Toxigenic Vibrio cholerae serogroup O1 and O139 are the pathogens responsible for the global cholera epidemic. V. cholerae can settle in the water and spread via the fecal-oral route. Rapid and accurate monitoring of live V. cholerae in environmental water has become an important strategy to prevent and control cholera transmission. Conventional plate counting is widely used to detect viable bacteria but requires time and effort. Methods This study aims to develop a new assay that combines triplex droplet digital PCR (ddPCR) with propidium monoazide (PMA) treatment for quantitatively detecting live V. cholerae O1/O139 and cholera enterotoxin. Specific primers and probes were designed according to the conserved regions of gene rfb O1, rfb O139, and ctxA. The amplification procedures and PMA treatment conditions were optimized. The specificity, sensitivity, and ability of PMA-ddPCR to detect viable bacteria-derived DNA were evaluated in simulated seawater samples. Results and Discussion The results revealed that the optimal primer concentrations of rfb O1, rfb O139, and ctxA were 1 μM, while the concentrations of the three probes were 0.25, 0.25, and 0.4 μM, respectively. The best annealing temperature was 58°C to obtain the most accurate results. The optimal strategy for distinguishing dead and live bacteria from PMA treatment was incubation at the concentration of 20 μM for 15 min, followed by exposure to a 650-W halogen lamp for 20 min. In pure culture solutions, the limit of detection (LODs) of V. cholerae O1 and O139, and ctxA were 127.91, 120.23 CFU/mL, and 1.5 copies/reaction in PMA-triplex ddPCR, respectively, while the LODs of the three targets were 150.66, 147.57 CFU/mL, and 2 copies/reaction in seawater samples. The PMA-ddPCR sensitivity was about 10 times higher than that of PMA-qPCR. When detecting spiked seawater samples with live bacterial concentrations of 1.53 × 102 and 1.53 × 105 CFU/mL, the assay presented a higher sensitivity (100%, 16/16) than qPCR (50.00%, 8/16) and a perfect specificity (100%, 9/9). These results indicate that the developed PMA-triplex ddPCR is superior to the qPCR regarding sensitivity and specificity and can be used to rapidly detect viable toxigenic V. cholerae O1 and O139 in suspicious seawater samples.
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Affiliation(s)
- Jinsong Yang
- Fujian Center for Disease Control and Prevention, Fuzhou, China
- Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Haibin Xu
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Zili Ke
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Naipeng Kan
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Enhui Zheng
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Yufeng Qiu
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Mengying Huang
- Fujian Center for Disease Control and Prevention, Fuzhou, China
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Flores-Ramírez A, Ortega-Cuenca J, Cuetero-Martínez Y, de Los Cobos D, Noyola A. Viability and removal assessment of Escherichia coli and Salmonella spp. by real-time PCR with propidium monoazide in the hygienization of sewage sludge using three anaerobic processes. WASTE MANAGEMENT (NEW YORK, N.Y.) 2023; 161:254-262. [PMID: 36907017 DOI: 10.1016/j.wasman.2023.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/31/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Sewage sludge should be stabilized for its beneficial use and pathogens, among other factors, should comply with environmental regulations. Three sludge stabilization process were compared to assess their suitability for producing Class A biosolids: MAD-AT (mesophilic (37 °C) anaerobic digestion (MAD) followed by an alkaline treatment (AT)); TAD (thermophilic (55 °C) anaerobic digester); and TP-TAD (mild thermal (80 °C, 1 h) pretreatment (TP) followed by a TAD). E. coli and Salmonella spp. were determined, differentiating three possible states: total cells (qPCR), viable cells using the propidium monoazide method (PMA-qPCR), and culturable cells (MPN). Culture techniques followed by the confirmative biochemical tests identified the presence of Salmonella spp. in PS and MAD samples, while the molecular methods (qPCR and PMA-qPCR) showed negative results in all samples. The TP + TAD arrangement reduced the concentration of total and viable E. coli cells in a greater extent than the TAD process. However, an increase of culturable E. coli was observed in the corresponding TAD step, indicating that the mild thermal pretreatment induced the viable but non-culturable state in E. coli. In addition, the PMA technique did not discriminate viable from non-viable bacteria in complex matrices. The three processes produced Class A biosolids (fecal coliforms < 1000 MPN/gTS and Salmonella spp, < 3 MPN/gTS) maintaining compliance after a 72 h storage period. It appears that the TP step favors the viable but not culturable state in E. coli cells, a finding that should be considered when adopting mild thermal treatment in sludge stabilization process arrangements.
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Affiliation(s)
- A Flores-Ramírez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México
| | - J Ortega-Cuenca
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México
| | - Y Cuetero-Martínez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México
| | - D de Los Cobos
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México
| | - A Noyola
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, Circuito Escolar, Ciudad Universitaria, Coyoacán 04510, Ciudad de México, México.
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24
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Rajabi A, Farajzadeh D, Dehghanzadeh R, Aslani H, Mosaferi M, Mousavi S, Shanehbandi D, Asghari FB. Optimizing ozone dose and contact time for removal of antibiotic-resistant P. aeruginosa, A. baumannii, E. coli, and associated resistant genes in effluent of an activated sludge process in a municipal WWTP. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:55569-55581. [PMID: 36897448 DOI: 10.1007/s11356-023-26270-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
This study aimed to investigate the impact of ozonation on inactivation of antibiotic-resistant bacteria (ARB) including E. coli, P. aeruginosa, and A. baumannii, as well as on removal of 16S-rRNA gene and their associated antibiotic-resistant genes (ARGs) indigenously present in effluent of municipal wastewater treatment plant. The Chick-Watson model was used to describe bacterial inactivation rates at specific ozone doses. Maximum reduction of total cultivable A. baumannii, E. coli, and P. aeruginosa were found to be 7.6, 7.1, and 4.7 log, respectively, with the highest ozone dose of 0.48 gO3/gCOD at 12 min contact time. According to the study results, complete inactivation of ARB and bacterial regrowth was not observed after 72 h incubation. The culture methods overestimated the performance of disinfection processes and propidium monoazide combined with qPCR, and showed the presence of viable but non-culturable bacteria after ozonation. ARGs were more persistent to ozone than ARB. The results of this study highlighted the significance of specific ozone dose and contact time in ozonation process considering the bacterial species and associated ARGs as well as the wastewater physicochemical characteristics, in order to help diminish the entrance of the biological microcontaminants into the environment.
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Affiliation(s)
- Akbar Rajabi
- Health and Environment Research Center, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Davoud Farajzadeh
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Reza Dehghanzadeh
- Health and Environment Research Center, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Hassan Aslani
- Health and Environment Research Center, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Mosaferi
- Health and Environment Research Center, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeid Mousavi
- Department of Statistics and Epidemiology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Dariush Shanehbandi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzaneh Baghal Asghari
- Department of Environmental Health Engineering, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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25
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Liu F, Lu H, Dong B, Huang X, Cheng H, Qu R, Hu Y, Zhong L, Guo Z, You Y, Xu ZZ. Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/– Bacteria. mSystems 2023; 8:e0073822. [PMID: 36971593 PMCID: PMC10134872 DOI: 10.1128/msystems.00738-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing technologies and downstream bioinformatic analyses, we gained an insight into the high-resolution microbial community composition of human saliva and feces, yet we know very little about whether such community DNA sequences represent viable microbes.
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26
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Chan SH, Liau SH, Low YJ, Chng KR, Wu Y, Chan JSH, Tan LK. A Real-Time PCR Approach for Rapid Detection of Viable Salmonella Enteritidis in Shell Eggs. Microorganisms 2023; 11:microorganisms11040844. [PMID: 37110268 PMCID: PMC10143610 DOI: 10.3390/microorganisms11040844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
Rapid and robust detection assays for Salmonella Enteritidis (SE) in shell eggs are essential to enable a quick testing turnaround time (TAT) at the earliest checkpoint and to ensure effective food safety control. Real-time polymerase chain reaction (qPCR) assays provide a workaround for the protracted lead times associated with conventional Salmonella diagnostic testing. However, DNA-based analysis cannot reliably discriminate between signals from viable and dead bacteria. We developed a strategy based on an SE qPCR assay that can be integrated into system testing to accelerate the detection of viable SE in egg-enriched cultures and verify the yielded SE isolates. The specificity of the assay was evaluated against 89 Salmonella strains, and SE was accurately identified in every instance. To define the indicator for a viable bacteria readout, viable or heat-inactivated SE were spiked into shell egg contents to generate post-enriched, artificially contaminated cultures to establish the quantification cycle (Cq) for viable SE. Our study has demonstrated that this technique could potentially be applied to accurately identify viable SE during the screening stage of naturally contaminated shell eggs following enrichment to provide an early alert, and that it consistently identified the serotypes of SE isolates in a shorter time than conventional testing.
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Affiliation(s)
- Siew Herng Chan
- National Centre for Food Science, Singapore Food Agency, 7 International Business Park, Singapore 609919, Singapore
| | - Sock Hwee Liau
- National Centre for Food Science, Singapore Food Agency, 7 International Business Park, Singapore 609919, Singapore
| | - Ying Jia Low
- National Centre for Food Science, Singapore Food Agency, 7 International Business Park, Singapore 609919, Singapore
| | - Kern Rei Chng
- National Centre for Food Science, Singapore Food Agency, 7 International Business Park, Singapore 609919, Singapore
| | - Yuansheng Wu
- National Centre for Food Science, Singapore Food Agency, 7 International Business Park, Singapore 609919, Singapore
| | - Joanne Sheot Harn Chan
- National Centre for Food Science, Singapore Food Agency, 7 International Business Park, Singapore 609919, Singapore
- Department of Food Science and Technology, National University of Singapore, S14 Level 5 Science Drive 2, Singapore 117542, Singapore
| | - Li Kiang Tan
- National Centre for Food Science, Singapore Food Agency, 7 International Business Park, Singapore 609919, Singapore
- Correspondence: ; Tel.: +65-6019-5826
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Rodríguez-Díaz C, Martín-Reyes F, Taminiau B, Ho-Plágaro A, Camargo R, Fernandez-Garcia F, Pinazo-Bandera J, Toro-Ortiz JP, Gonzalo M, López-Gómez C, Rodríguez-Pacheco F, Rodríguez de los Ríos D, Daube G, Alcain-Martinez G, García-Fuentes E. The Metagenomic Composition and Effects of Fecal-Microbe-Derived Extracellular Vesicles on Intestinal Permeability Depend on the Patient's Disease. Int J Mol Sci 2023; 24:ijms24054971. [PMID: 36902401 PMCID: PMC10002483 DOI: 10.3390/ijms24054971] [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: 01/10/2023] [Revised: 02/14/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
The composition and impact of fecal-microbe-derived extracellular vesicles (EVs) present in different diseases has not been analyzed. We determined the metagenomic profiling of feces and fecal-microbe-derived EVs from healthy subjects and patients with different diseases (diarrhea, morbid obesity and Crohn's disease (CD)) and the effect of these fecal EVs on the cellular permeability of Caco-2 cells. The control group presented higher proportions of Pseudomonas and Rikenellaceae_RC9_gut_group and lower proportions of Phascolarctobacterium, Veillonella and Veillonellaceae_ge in EVs when compared with the feces from which these EVs were isolated. In contrast, there were significant differences in 20 genera between the feces and EV compositions in the disease groups. Bacteroidales and Pseudomonas were increased, and Faecalibacterium, Ruminococcus, Clostridium and Subdoligranum were decreased in EVs from control patients compared with the other three groups of patients. Tyzzerella, Verrucomicrobiaceae, Candidatus_Paracaedibacter and Akkermansia were increased in EVs from the CD group compared with the morbid obesity and diarrhea groups. Fecal EVs from the morbid obesity, CD and, mainly, diarrhea induced a significant increase in the permeability of Caco-2 cells. In conclusion, the metagenomic composition of fecal-microbe-derived EVs changes depending on the disease of the patients. The modification of the permeability of Caco-2 cells produced by fecal EVs depends on the disease of the patients.
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Affiliation(s)
- Cristina Rodríguez-Díaz
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Flores Martín-Reyes
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
- Facultad de Medicina, Universidad de Málaga, 29010 Malaga, Spain
| | - Bernard Taminiau
- Fundamental and Applied Research for Animals & Health (FARAH), Department of Food Microbiology, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Ailec Ho-Plágaro
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Raquel Camargo
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Felix Fernandez-Garcia
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - José Pinazo-Bandera
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Juan Pedro Toro-Ortiz
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Montserrat Gonzalo
- UCG de Endocrinología y Nutrición, Hospital Regional Universitario, 29009 Malaga, Spain
| | - Carlos López-Gómez
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Francisca Rodríguez-Pacheco
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Dámaris Rodríguez de los Ríos
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
| | - Georges Daube
- Fundamental and Applied Research for Animals & Health (FARAH), Department of Food Microbiology, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Guillermo Alcain-Martinez
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
- Correspondence: (G.A.-M.); (E.G.-F.)
| | - Eduardo García-Fuentes
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- UGC de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, 29010 Malaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 29010 Malaga, Spain
- Correspondence: (G.A.-M.); (E.G.-F.)
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Wang Y, Fang W, Wang X, Zhou L, Zheng G. Spatial distribution of fecal pollution indicators in sewage sludge flocs and their removal and inactivation as revealed by qPCR/viability-qPCR during potassium ferrate treatment. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130262. [PMID: 36327846 DOI: 10.1016/j.jhazmat.2022.130262] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/11/2022] [Accepted: 10/23/2022] [Indexed: 06/16/2023]
Abstract
Sludge reuse and utilization is one of important routines of disseminating fecal pollution to surface water and groundwater. However, it remains unclear the spatial distribution of fecal pollution indicators in sludge flocs and their reductions during sludge treatment processes. In this study, the abundances of fecal pollution indicators including cross-assembly phage (crAssphage), JC and BK polyomavirus (JCPyV, BKPyV), human adenovirus (HAdV), the human-specific HF183 Bacteroides (HF183) and Escherichia coli (EC) in soluble extracellular polymeric substances (S-EPS), loosely-bound EPS (LB-EPS), tightly-bound EPS (TB-EPS), and pellets of sludge flocs were determined, and the effect of potassium ferrate (PF) treatment on their removal and inactivation was investigated by using both qPCR and viability-qPCR. Results showed that all investigated indicators were detected in each fraction of sludge flocs. The PF treatment led to a great migration of indicators from sludge pellets to sludge EPS and some extent of their inactivation in each fraction of sludge flocs. The overall reductions of human fecal indicators in sludge determined by qPCR were 0-1.30 logs, which were 0-2 orders of magnitude lower than those of 0.69-2.39 logs detected by viability-qPCR, implying their inactivation by PF treatment to potentially alleviate the associated human health risks.
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Affiliation(s)
- Yuhang Wang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; College of Materials and Chemical Engineering, Pingxiang University, Pingxiang 337055, China
| | - Wenhao Fang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinxin Wang
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lixiang Zhou
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China
| | - Guanyu Zheng
- Department of Environmental Engineering, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China; Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing 210095, China.
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29
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Cuetero-Martínez Y, Flores-Ramírez A, De Los Cobos-Vasconcelos D, Aguirre-Garrido JF, López-Vidal Y, Noyola A. Removal of bacterial pathogens and antibiotic resistance bacteria by anaerobic sludge digestion with thermal hydrolysis pre-treatment and alkaline stabilization post-treatment. CHEMOSPHERE 2023; 313:137383. [PMID: 36436581 DOI: 10.1016/j.chemosphere.2022.137383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/16/2023]
Abstract
Primary sludge (PS) is associated with public health and environmental risks, so regulations focus on reducing the pathogenic and heavy metal contents of the treated material (biosolids), intended for soil amendments and land reclamation. The regulations set limits for Escherichia coli (or fecal coliforms), Salmonella spp., helminth eggs and enterovirus. However, the potential risk due to antibiotic resistant bacteria (ARB) and other human potential pathogenic bacteria (HPB) are not considered. In this work, three sludge treatment processes, having in common an anaerobic digestion step, were applied to assess the removal of regulated bacteria (fecal coliforms, Salmonella spp), ARB and HPB. The treatment arrangements, fed with PS from a full-scale wastewater treatment plant were: 1) Mesophilic anaerobic digestion followed by alkaline stabilization post-treatment (MAD-CaO); 2) Thermophilic anaerobic digestion (TAD) and, 3) Pre-treatment (mild thermo-hydrolysis) followed by TAD (PT-TAD). The results address the identification, quantification (colony forming units) and taxonomic characterization of ARB resistant to β-lactams and vancomycin, as well as the taxonomic characterization of HPB by sequencing with PacBio. In addition, quantification based on culture media of fecal coliforms and Salmonella spp. is presented. The capabilities and limitations of microbiological and metataxonomomic analyses based on PacBio sequencing are discussed, emphasizing that they complement each other. Genus Aeromonas, Acinetobacter, Citrobacter, Enterobacter, Escherichia, Klebsiella, Ochrobactrum, Pseudomonas and Raoultella, among others, were found in the PS, which are of clinical or environmental importance, being either HPB, HPB-ARB, or non-pathogenic ARB with the potentiality of horizontal gene transfer. Based on the analysis of fecal coliforms and Salmonella spp., the three processes produced class A (highest) biosolids, suitable for unrestricted agriculture applications. Mild thermo-hydrolisis was effective in decreasing ARB cultivability, but it reappeared after the following TAD. O. intermedium (HPB-ARB) was enriched in MAD and TAD while Laribacter hongkongensis (HPB) did persist after the applied treatments.
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Affiliation(s)
- Yovany Cuetero-Martínez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico; Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - Aarón Flores-Ramírez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - Daniel De Los Cobos-Vasconcelos
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - José Félix Aguirre-Garrido
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana - Unidad Lerma, 52005 Lerma de Villada, Edo. Mex, Mexico
| | - Yolanda López-Vidal
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - Adalberto Noyola
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico.
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Nisar MA, Ross KE, Brown MH, Bentham R, Best G, Whiley H. Detection and quantification of viable but non-culturable Legionella pneumophila from water samples using flow cytometry-cell sorting and quantitative PCR. Front Microbiol 2023; 14:1094877. [PMID: 36793878 PMCID: PMC9922708 DOI: 10.3389/fmicb.2023.1094877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/03/2023] [Indexed: 02/03/2023] Open
Abstract
Legionella pneumophila is a waterborne pathogen and, as the causative agent of Legionnaires' disease, a significant public health concern. Exposure to environmental stresses, and disinfection treatments, promotes the formation of resistant and potentially infectious viable but non-culturable (VBNC) Legionella. The management of engineered water systems to prevent Legionnaires' disease is hindered by the presence of VBNC Legionella that cannot be detected using the standard culture (ISO11731:2017-05) and quantitative polymerase reaction (ISO/TS12869:2019) methods. This study describes a novel method to quantify VBNC Legionella from environmental water samples using a "viability based flow cytometry-cell sorting and qPCR" (VFC + qPCR) assay. This protocol was then validated by quantifying the VBNC Legionella genomic load from hospital water samples. The VBNC cells were unable to be cultured on Buffered Charcoal Yeast Extract (BCYE) agar; however, their viability was confirmed through their ATP activity and ability to infect amoeba hosts. Subsequently, an assessment of the ISO11731:2017-05 pre-treatment procedure demonstrated that acid or heat treatment cause underestimation of alive Legionella population. Our results showed that these pre-treatment procedures induce culturable cells to enter a VBNC state. This may explain the observed insensitivity and lack of reproducibility often observed with the Legionella culture method. This study represents the first time that flow cytometry-cell sorting in conjunction with a qPCR assay has been used as a rapid and direct method to quantify VBNC Legionella from environmental sources. This will significantly improve future research evaluating Legionella risk management approaches for the control of Legionnaires' disease.
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Affiliation(s)
- Muhammad Atif Nisar
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Kirstin E. Ross
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Melissa H. Brown
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Richard Bentham
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Giles Best
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia,Flow Cytometry Facility, Flinders University, Bedford Park, SA, Australia
| | - Harriet Whiley
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia,*Correspondence: Harriet Whiley, ✉
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Shehata HR, Hassane B, Newmaster SG. Real-time polymerase chain reaction methods for strain specific identification and enumeration of strain Lacticaseibacillus paracasei 8700:2. Front Microbiol 2023; 13:1076631. [PMID: 36741903 PMCID: PMC9889646 DOI: 10.3389/fmicb.2022.1076631] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
Introduction Reliable and accurate methods for probiotic identification and enumeration, at the strain level plays a major role in confirming product efficacy since probiotic health benefits are strain-specific and dose-dependent. In this study, real-time PCR methods were developed for strain specific identification and enumeration of L. paracasei 8700:2, a probiotic strain that plays a role in fighting the common cold. Methods The assay was designed to target a unique region in L. paracasei 8700:2 genome sequence to achieve strain level specificity. The identification assay was evaluated for specificity and sensitivity. The enumeration viability real-time PCR (v-qPCR) method was first optimized for the viability treatment, then the method was evaluated for efficiency, limit of quantification, precision, and its performance was compared to plate count (PC) and viability droplet digital PCR (v-ddPCR) methods. Results The identification method proved to be strain specific and highly sensitive with a limit of detection of 0.5 pg of DNA. The optimal viability dye (PMAxx) concentration was 50 μM. The method was efficient (> 90% with R 2 values > 0.99), with a linear dynamic range between 6*102 and 6*105 copies. The method was highly precise with a relative standard deviation below 5%. The Pearson correlation coefficient (r) was 0.707 for PC and v-qPCR methods, and 0.922 for v-qPCR and v-ddPCR. Bland-Altman method comparison showed that v-qPCR always gave higher values compared to PC method (relative difference ranging from 119% to 184%) and showed no consistent trend (relative difference ranging from -20% to 22%) when comparing v-qPCR and v-ddPCR methods. Discussion The difference between PC and v-PCR methods can potentially be attributed to the proportion of cells that exist in a viable but non culturable (VBNC) state, which can be count by v-PCR but not with PC. The developed v-qPCR method was confirmed to be strain specific, sensitive, efficient, with low variance, able to count VBNC cells, and has shorter time to results compared to plate count methods. Thus, the identification and enumeration methods developed for L. paracasei 8700:2 will be of great importance to achieve high quality and efficacious probiotic products.
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Affiliation(s)
- Hanan R. Shehata
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada,Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt,Purity-IQ Inc., Guelph, ON, Canada,*Correspondence: Hanan R. Shehata,
| | | | - Steven G. Newmaster
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
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Loublier C, Taminiau B, Heinen J, Lecoq L, Amory H, Daube G, Cesarini C. Evaluation of Bacterial Composition and Viability of Equine Feces after Processing for Transplantation. Microorganisms 2023; 11:microorganisms11020231. [PMID: 36838196 PMCID: PMC9966902 DOI: 10.3390/microorganisms11020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Fecal microbiota transplantation (FMT) has been used empirically for decades in equine medicine to treat intestinal dysbiosis but evidence-based information is scarce. This in vitro study aimed at assessing the effect of a commonly used pre-FMT processing method on the bacterial composition and viability of the fecal filtrate. Three samples of fresh equine manure (T0) were processed identically: the initial manure was mixed with 1 L of lukewarm water and chopped using an immersion blender to obtain a mixture (T1), which was left uncovered during 30 min (T2) and percolated through a sieve to obtain a fecal filtrate (T3). Samples were taken throughout the procedure (Tn) and immediately stored at 4 °C until processing. The 16S rDNA amplicon profiling associated with propidium monoazide treatment was performed on each sample to select live bacteria. Analyses of α and β diversity and main bacterial populations and quantitative (qPCR) analysis were performed and statistically compared (significance p < 0.05) between time points (T0-T3). No significant differences in ecological indices or mean estimated total living bacteria were found in the final fecal filtrate (T3) in regard to the original manure (T0); however, relative abundances of some minor genera (Fibrobacter, WCHB1-41_ge and Akkermansia) were significantly different in the final filtrate. In conclusion, the results support the viability of the major bacterial populations in equine feces when using the described pre-FMT protocol.
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Affiliation(s)
- Clémence Loublier
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Bernard Taminiau
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
- Department of Food Sciences—Microbiology, Faculty of Veterinary Medicine, University of Liege, Avenue de Cureghem 10, Bât. B43b, 4000 Liège, Belgium
| | - Julia Heinen
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Laureline Lecoq
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Hélène Amory
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Georges Daube
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
- Department of Food Sciences—Microbiology, Faculty of Veterinary Medicine, University of Liege, Avenue de Cureghem 10, Bât. B43b, 4000 Liège, Belgium
| | - Carla Cesarini
- Equine Clinical Department, Faculty of Veterinary Medicine, University of Liège, Bât. B41, 4000 Liège, Belgium
- Fundamental and Applied Research for Animals & Health (FARAH), Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
- Correspondence:
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Rausch F, Tanneberger F, Abd El Wahed A, Truyen U. Validation of the efficacy of air purifiers using molecular techniques. PLoS One 2023; 18:e0280243. [PMID: 36622844 PMCID: PMC9829175 DOI: 10.1371/journal.pone.0280243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/23/2022] [Indexed: 01/10/2023] Open
Abstract
The importance of air purifiers has increased in recent years, especially with the "coronavirus disease 2019" pandemic. The efficacy of air purifiers is usually determined under laboratory conditions before widespread application. The standard procedure for testing depends on virus cultivation and titration on cell culture. This, however, requires several days to deliver results. The aim of this study was to establish a rapid molecular assay which can differentiate between intact infectious and distorted non-infectious virus particles. Feline Coronavirus was selected as model for screening. First the samples were pretreated with enzymes (universal nuclease and RNase cocktail enzyme mixture) or viability dye (propidium monoazide) to eliminate any free nucleic acids. The ribonucleic acid (RNA) from intact virus was released via magnetic beads-based extraction, then the amount of the RNA was determined using real-time reverse transcription polymerase chain reaction (RT-PCR) or reverse transcription recombinase-aided amplification (RT-RAA). All results were compared to the infectivity assay based on the calculation of the 50% tissue culture infectious dose (TCID50). The nuclease has eliminated 100% of the free Feline Coronavirus RNA, while propidium monoazide underperformed (2.3-fold decrease in free RNA). Both RT-RAA and real-time RT-PCR produced similar results to the infectivity assay on cell culture with limit of detection of 102 TCID50/mL. Two UV-C air purifiers with prosperities of 100% inactivation of the viruses were used to validate the established procedure. Both real-time RT-PCR and RT-RAA were able to differentiate between intact virus particles and free RNA. To conclude, this study revealed a promising rapid method to validate the efficacy of air purifiers by combining enzymatic pretreatment and molecular assays.
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Affiliation(s)
- Finja Rausch
- Faculty of Veterinary Medicine, Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Leipzig, Germany
| | - Franziska Tanneberger
- Faculty of Veterinary Medicine, Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Leipzig, Germany
| | - Ahmed Abd El Wahed
- Faculty of Veterinary Medicine, Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Leipzig, Germany
- * E-mail:
| | - Uwe Truyen
- Faculty of Veterinary Medicine, Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, Leipzig, Germany
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Shen J, McFarland AG, Blaustein RA, Rose LJ, Perry-Dow KA, Moghadam AA, Hayden MK, Young VB, Hartmann EM. An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics. MICROBIOME 2022; 10:206. [PMID: 36457108 PMCID: PMC9716758 DOI: 10.1186/s40168-022-01412-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Effective surveillance of microbial communities in the healthcare environment is increasingly important in infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but are currently challenged by several limitations: (1) they are not powerful enough to extract valid signals out of the background noise for low-biomass samples, (2) they do not distinguish between viable and nonviable organisms, and (3) they do not reveal the microbial load quantitatively. An additional practical challenge towards a robust pipeline is the inability to efficiently allocate sequencing resources a priori. Assessment of sequencing depth is generally practiced post hoc, if at all, for most microbiome studies, regardless of the sample type. This practice is inefficient at best, and at worst, poor sequencing depth jeopardizes the interpretation of study results. To address these challenges, we present a workflow for metagenomics-based environmental surveillance that is appropriate for low-biomass samples, distinguishes viability, is quantitative, and estimates sequencing resources. RESULTS The workflow was developed using a representative microbiome sample, which was created by aggregating 120 surface swabs collected from a medical intensive care unit. Upon evaluating and optimizing techniques as well as developing new modules, we recommend best practices and introduce a well-structured workflow. We recommend adopting liquid-liquid extraction to improve DNA yield and only incorporating whole-cell filtration when the nonbacterial proportion is large. We suggest including propidium monoazide treatment coupled with internal standards and absolute abundance profiling for viability assessment and involving cultivation when demanding comprehensive profiling. We further recommend integrating internal standards for quantification and additionally qPCR when we expect poor taxonomic classification. We also introduce a machine learning-based model to predict required sequencing effort from accessible sample features. The model helps make full use of sequencing resources and achieve desired outcomes. Video Abstract CONCLUSIONS: This workflow will contribute to more accurate and robust environmental surveillance and infection prevention. Lessons gained from this study will also benefit the continuing development of methods in relevant fields.
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Affiliation(s)
- Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA.
| | - Alexander G McFarland
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
| | - Ryan A Blaustein
- Department of Nutrition and Food Science, University of Maryland, College Park, USA
| | - Laura J Rose
- Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Anahid A Moghadam
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
| | - Mary K Hayden
- Division of Infectious Diseases, Department of Internal Medicine, Rush Medical College, Chicago, USA
| | - Vincent B Young
- Department of Internal Medicine/Division of Infectious Diseases, The University of Michigan Medical School, Ann Arbor, USA
| | - Erica M Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, 60208-3109, USA
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Boschi G, Piccinelli G, Bonfanti C, Salgarello SA. Ex-vivo study about antimicrobial effectiveness of phytic acid against Enterococcus faecalis into root canals. Minerva Dent Oral Sci 2022; 71:299-307. [PMID: 36760199 DOI: 10.23736/s2724-6329.22.04614-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
BACKGROUND Endodontic failure is due to the persistence of microorganisms, especially Enterococcus faecalis, which have become resistant to disinfection measures. Sodium hypochlorite has been traditionally used, whereas phytic acid, a natural irrigant, needs to be further investigated. METHODS This ex-vivo study compared the antibacterial effectiveness of 0.9% saline solution, 5% sodium hypochlorite and 5% phytic acid against Enterococcus faecalis ATCC 29212 into the apical root canal third of 96 single-rooted extracted teeth, after 1-minute push-and-pull irrigation - a basic irrigation technique. Survived microorganisms were evaluated both through a traditional colony-forming-unit count and introducing the viability PCR, which precisely detects only DNA from intact cells: dead and damaged cells were excluded thanks to a propidium monoazide dye. RESULTS The culture methods showed that 5% sodium hypochlorite (median: 0 CFU/mL) has a significant greater antibacterial effectiveness (P<0.001) compared both to 0.9% saline solution (median: 4.76 CFU/mL) and 5% phytic acid (median: 0.25 CFU/mL). However, 5% phytic acid proved to be significantly more effective (P<0.001) than 0.9% saline solution. The viability PCR did not reveal a significant difference between 5% sodium hypochlorite (median: 4.12×104 survived bacteria) and 0.9% saline solution (median: 8.45×104 survived bacteria). Five percent phytic acid (median: 0.83×104 survived bacteria) was significantly more effective than both 0.9% saline solution (P<0.001) and 5% sodium hypochlorite (P<0.001). CONCLUSIONS The findings suggest that 5% phytic acid works against root canal bacteria even with a basic irrigation technique and viability PCR seems to lead to more reliable and sensitive data rather than the culture methods.
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Affiliation(s)
- Giulia Boschi
- School of Dentistry, Department of Medical and Surgery Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy -
| | - Giorgio Piccinelli
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Carlo Bonfanti
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Stefano A Salgarello
- School of Dentistry, Department of Medical and Surgery Specialties, Radiological Sciences and Public Health, University of Brescia, Brescia, Italy
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Bolzon V, Pesando M, Bulfoni M, Nencioni A, Nencioni E. An Integrated Analytical Approach for the Characterization of Probiotic Strains in Food Supplements. Nutrients 2022; 14:nu14235085. [PMID: 36501115 PMCID: PMC9736879 DOI: 10.3390/nu14235085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
Research surrounding health benefits from probiotics is becoming popular because of the increasing demand for safer products with protective and therapeutic effects. Proven benefits are species- or genus-specific; however, no certified assays are available for their characterization and quantification at the strain level in the food supplement industry. The objective of this study was to develop a strain-specific Real-time quantitative polymerase chain reaction (RT-qPCR)-based method to be implemented in routine tests for the identification and quantification of Bifidobacterium longum, Bifidobacterium animalis spp. lactis, Lactobacillus paracasei, Lactobacillus rhamnosus, Lactobacillus casei, Bifidobacterium breve, Lactobacillus acidophilus, Lactobacillus plantarum, and Lactobacillus helveticus, starting from a powder mixture of food supplements. The method optimization was carried out in combination with flow cytometry to compare results between the two strategies and implement the analytical workflow with the information also regarding cell viability. These assays were validated in accordance with the International Council for Harmonization of Technical Requirements for Pharmaceuticals for Human Use (ICH) criteria using the plate count enumeration as the gold standard reference. Briefly, probiotic DNAs were extracted from two powder food supplements. Strain-specific primers targeting unique sequence regions of 16S RNA were identified and amplified by RT-qPCR. Primers were tested for specificity, sensitivity, and efficiency. Both RT-qPCR and flow-cytometry methods described in our work for the quantification and identification of Lactobacillus and Bifidobacterium strains were specific, sensitive, and precise, showing better performances with respect to the morphological colony identification. This work demonstrated that RT-qPCR can be implemented in the quality control workflow of commercial probiotic products giving more standardized and effective results regarding species discrimination.
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Affiliation(s)
| | | | - Michela Bulfoni
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Alessandro Nencioni
- IBSA Institut Biochimique SA, Via del Piano 29, CH-6915 Pambio Noranco, Switzerland
| | - Emanuele Nencioni
- Biofarma Group Srl., Via Castelliere 2, 33036 Udine, Italy
- Correspondence:
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Thilakarathna SH, Stokowski T, Chui L. An Improved Real-Time Viability PCR Assay to Detect Salmonella in a Culture-Independent Era. Int J Mol Sci 2022; 23:ijms232314708. [PMID: 36499040 PMCID: PMC9738789 DOI: 10.3390/ijms232314708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022] Open
Abstract
Viability PCR (vPCR) uses a DNA intercalating dye to irreversibly bind double-stranded DNA from organisms with compromised cell membranes. This allows the selective amplification of DNA from intact cells. An optimized vPCR protocol should minimize false positives (DNA from compromised cells not fully removed) and false negatives (live cell DNA bound by the dye). We aimed to optimize a vPCR protocol using PMAxx™ as the intercalating agent and Salmonella Enteritidis as the target organism. To do this, we studied (1) single vs. sequential PMAxx™ addition; (2) a wash step post-PMAxx™ treatment; (3) a change of tube post-treatment before DNA extraction. The single vs. sequential PMAxx™ addition showed no difference. Results signified that PMAxx™ potentially attached to polypropylene tube walls and bound the released DNA from PMA-treated live cells when lysed in the same tube. A wash step was ineffective but transfer of the treated live cells to a new tube minimized these false-negative results. Our optimized protocol eliminated 108 CFU/mL heat-killed cell DNA in the presence of different live cell dilutions without compromising the amplification of the live cells, minimizing false positives. With further improvements, vPCR has great potential as a culture-independent diagnostic tool.
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Affiliation(s)
- Surangi H. Thilakarathna
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Taryn Stokowski
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 1C9, Canada
| | - Linda Chui
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB T6G 1C9, Canada
- Alberta Precision Laboratories, Public Health Laboratory (ProvLab), Edmonton, AB T6G 2J2, Canada
- Correspondence:
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Nasal microbiome disruption and recovery after mupirocin treatment in Staphylococcus aureus carriers and noncarriers. Sci Rep 2022; 12:19738. [PMID: 36396730 PMCID: PMC9671894 DOI: 10.1038/s41598-022-21453-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
Nasal decolonization procedures against the opportunistic pathogen Staphylococcus aureus rely on topical antimicrobial drug usage, whose impact on the nasal microbiota is poorly understood. We examined this impact in healthy S. aureus carriers and noncarriers. This is a prospective interventional cohort study of 8 S. aureus carriers and 8 noncarriers treated with nasal mupirocin and chlorhexidine baths. Sequential nasal swabs were taken over 6 months. S. aureus was detected by quantitative culture and genotyped using spa typing. RNA-based 16S species-level metabarcoding was used to assess the living microbial diversity. The species Dolosigranulum pigrum, Moraxella nonliquefaciens and Corynebacterium propinquum correlated negatively with S. aureus carriage. Mupirocin treatment effectively eliminated S. aureus, D. pigrum and M. nonliquefaciens, but not corynebacteria. S. aureus recolonization in carriers occurred more rapidly than recolonization by the dominant species in noncarriers (median 3 vs. 6 months, respectively). Most recolonizing S. aureus isolates had the same spa type as the initial isolate. The impact of mupirocin-chlorhexidine treatment on the nasal microbiota was still detectable after 6 months. S. aureus recolonization predated microbiota recovery, emphasizing the strong adaptation of this pathogen to the nasal niche and the transient efficacy of the decolonization procedure.
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Yang L, Long Y, Li Q, Song W, Huang Y, Liang G, Yu D, Zhou M, Xu G, Chen Y, Huang C, Tang X. Detection of suid herpesvirus 1 infectivity in pigs by propidium monoazide-qPCR. Front Vet Sci 2022; 9:975726. [DOI: 10.3389/fvets.2022.975726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/05/2022] [Indexed: 11/13/2022] Open
Abstract
At present, there is no effective experimental method for detecting whether the suid herpesvirus 1 (SHV-1) detected in pigs is infectious. Although the technique of quantitative polymerase chain reaction (qPCR) has significantly improved the detection rate and accuracy of the disease, it does not differentiate between infective and non-infective status of the virus. Propidium monoazide (PMA) is a dye that can be combined with DNA molecules. The decomposition of PMA produces an azene compound covalently crosslinked with DNA molecules, thereby inhibiting PCR amplification of DNA. In this study, the combination of PMA and qPCR was used to determine the infectivity of SHV-1. We optimized the method from the selection of primers, the working concentration of PMA, and the method of inactivation using UV or heat inactivation. We found that when specific primer 1 was used and a PMA working concentration was 50–100 μM, heat inactivation was able to distinguish whether SHV-1 was infectious or not. We also showed that UV prevented the virus from replicating, it did not destroy the capsid of the virus, and therefore, PMA cannot enter the virus and bind to the nucleic acid of the virus. Consequently, there is no way to identify the infectivity of the virus using UV inactivation. The study showed that the method was stable and the detection rate reached 96%. In conclusion, this method exhibited strong specificity and high sensitivity and can identify the infectivity of SHV-1. This method has practical significance for clinical virus isolation and the effects of disinfection of farms.
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40
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Stinson LF, Ma J, Sindi AS, Geddes DT. Methodological approaches for studying the human milk microbiome. Nutr Rev 2022; 81:705-715. [PMID: 36130405 DOI: 10.1093/nutrit/nuac082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human milk contains a low-biomass, low-diversity microbiome, consisting largely of bacteria. This community is of great research interest in the context of infant health and maternal and mammary health. However, this sample type presents many unique methodological challenges. In particular, there are numerous technical considerations relating to sample collection and storage, DNA extraction and sequencing, viability, and contamination. Failure to properly address these challenges may lead to distortion of bacterial DNA profiles generated from human milk samples, ultimately leading to spurious conclusions. Here, these technical challenges are discussed, and various methodological approaches used to address them are analyzed. Data were collected from studies in which a breadth of methodological approaches were used, and recommendations for robust and reproducible analysis of the human milk microbiome are proposed. Such methods will ensure high-quality data are produced in this field, ultimately supporting better research outcomes for mothers and infants.
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Affiliation(s)
- Lisa F Stinson
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Jie Ma
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Azhar S Sindi
- Division of Obstetrics and Gynaecology, School of Medicine, The University of Western Australia, Perth, Australia.,is with the College of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Donna T Geddes
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
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Rodrigo I, Ballesta C, Nunes EB, Pérez P, García-Arriaza J, Arias A. Eeyarestatin I, an inhibitor of the valosin-containing protein, exhibits potent virucidal activity against the flaviviruses. Antiviral Res 2022; 207:105416. [PMID: 36113629 DOI: 10.1016/j.antiviral.2022.105416] [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: 06/18/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/26/2022]
Abstract
Cellular responses to stress generally lead to the activation of the endoplasmic reticulum-associated protein degradation (ERAD) pathway. Several lines of study support that ERAD may be playing a proviral role during flaviviral infection. A key host factor in ERAD is the valosin-containing protein (VCP), an ATPase which ushers ubiquitin-tagged proteins to degradation by the proteasome. VCP exhibits different proviral activities, such as engaging in the biogenesis of viral replication organelles and facilitating flavivirus genome uncoating after the viral particle entry. To investigate the possible antiviral value of drugs targeting VCP, we tested two inhibitors: eeyarestatin I (EEY) and xanthohumol (XAN). Both compounds were highly effective in suppressing Zika virus (ZIKV) and Usutu virus (USUV) replication during infection in cell culture. Further analysis revealed an unexpected virucidal activity for EEY, but not for XAN. Preincubation of ZIKV or USUV with EEY before inoculation to cells resulted in significant decreases in infectivity in a dose- and time-dependent manner. Viral genomes in samples previously treated with EEY were more sensitive to propidium monoazide, an intercalating agent, with 10- to 100-fold decreases observed in viral RNA levels, supporting that EEY affects viral particle integrity. Altogether, these results support that EEY is a strong virucide against two unrelated flaviviruses, encouraging further studies to investigate its potential use as a broad-acting drug or the development of improved derivatives in the treatment of flaviviral infection.
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Affiliation(s)
- Imanol Rodrigo
- Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomedicas (CRIB), Universidad de Castilla-La Mancha (UCLM), Albacete, Spain; Unidad de Biomedicina, UCLM-CSIC, Albacete, Spain
| | - Carlos Ballesta
- Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomedicas (CRIB), Universidad de Castilla-La Mancha (UCLM), Albacete, Spain; Unidad de Biomedicina, UCLM-CSIC, Albacete, Spain
| | - Eliane Blanco Nunes
- Departamento de Vigilância em Zoonoses, Secretaria Municipal de Saúde Goiânia, Rodovia Go-020 km 08, Val Das Pombas, 75250-000, Goiânia, Goias State, Brazil
| | - Patricia Pérez
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnologla (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain; Centro de Investigacion Biomedica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Juan García-Arriaza
- Department of Molecular and Cellular Biology, Centro Nacional de Biotecnologla (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain; Centro de Investigacion Biomedica en Red de Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Armando Arias
- Unidad de Medicina Molecular, Centro Regional de Investigaciones Biomedicas (CRIB), Universidad de Castilla-La Mancha (UCLM), Albacete, Spain; Unidad de Biomedicina, UCLM-CSIC, Albacete, Spain; Escuela Técnica Superior de Ingenieros Agrónomos, UCLM, Albacete, Spain.
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Inoue D, Hiroshima N, Nakamura S, Ishizawa H, Ike M. Characterization of Two Novel Predatory Bacteria, Bacteriovorax stolpii HI3 and Myxococcus sp. MH1, Isolated from a Freshwater Pond: Prey Range, and Predatory Dynamics and Efficiency. Microorganisms 2022; 10:1816. [PMID: 36144418 PMCID: PMC9505378 DOI: 10.3390/microorganisms10091816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Predatory bacteria, which prey on other bacteria, have significant functions in microbial ecosystems and have attracted increasing attention for their biotechnological use. However, knowledge of the characteristics of wild-type environmental predatory bacteria remains limited. This study isolated two predatory bacteria, Bacteriovorax stolpii HI3 and Myxococcus sp. MH1, from a freshwater pond and characterized their predation capabilities. Determination of the prey range using 53 potential prey strains, including 52 environmental strains, revealed that B. stolpii HI3 and Myxococcus sp. MH1 could prey on a wide spectrum of Gram-negative bacteria and a broader range of bacteria, irrespective of phylogeny, in accordance with the common characteristics of Bdellovibrio and like organisms and myxobacteria, respectively. Liquid culture assays also found that although predation by B. stolpii HI3 rapidly and largely occurred, the prey bacteria regrew, possibly through plastic phenotypic resistance to predation. In contrast, predation by Myxococcus sp. MH1 occurred at relatively low efficiency but was longer lasting. The two strains exhibited slightly distinct temperature preferences but commonly preferred slightly alkaline pH. The novel findings of this study provide evidence for the coexistence of predatory bacteria with diverse predation capabilities in the natural aquatic environment.
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Affiliation(s)
- Daisuke Inoue
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Naoto Hiroshima
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - So Nakamura
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
| | - Hidehiro Ishizawa
- Department of Applied Chemistry, University of Hyogo, 2167 Shosha, Himeji 671-2280, Japan
| | - Michihiko Ike
- Division of Sustainable Energy and Environmental Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
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Shi Z, Li X, Fan X, Xu J, Liu Q, Wu Z, Pan D. PMA-qPCR method for the selective quantitation of viable lactic acid bacteria in fermented milk. Front Microbiol 2022; 13:984506. [PMID: 36160254 PMCID: PMC9491339 DOI: 10.3389/fmicb.2022.984506] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
The number of viable lactic acid bacteria (LAB) is a key indicator of the quality of fermented milk. Currently, the combination of propidium monoazide (PMA) and qPCR has been applied in the quantification of viable bacteria in various matrices. In this research, the PMA-qPCR method was used to detect the number of viable bacteria of each LAB species in fermented milk. By analyzing pheS gene and 16S rRNA gene sequence similarities in five species of LAB, namely Lactobacillus delbrueckii subsp. bulgaricus, Lactiplantibacillus plantarum, Streptococcus thermophilus, Lactobacillus helveticus, and Lactococcus lactis subsp. lactis, the pheS gene resolved species identities better and was thus selected to design specific primers and probes. The pheS gene was cloned into the pUC19 vector and used to construct a standard curve for absolute quantification. Standard curves for quantification were constructed for each LAB species for serial dilutions between 1011 and 106 CFU/mL, with R2 > 0.99. The number of viable bacteria in the fermented milk detected by PMA-qPCR was significantly lower than that of qPCR (P < 0.05), indicating that PMA inhibited the amplification of DNA from dead cells. This was corroborated by the results from bacterial staining and plate count experiments. The proposed PMA-qPCR method provided rapid qualitative and quantitative determination of the number of viable bacteria for each LAB species in fermented milk within 3 h.
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Affiliation(s)
- Zihang Shi
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Xiefei Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Xiankang Fan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Jue Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
| | - Qing Liu
- Nanjing Dairy Group, Nanjing, China
| | - Zhen Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
- *Correspondence: Zhen Wu,
| | - Daodong Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China
- Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, China
- Daodong Pan,
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Wang H, Shankar V, Jiang X. Compositional and Functional Changes in Microbial Communities of Composts Due to the Composting-Related Factors and the Presence of Listeria monocytogenes. Microbiol Spectr 2022; 10:e0184521. [PMID: 35703536 PMCID: PMC9430276 DOI: 10.1128/spectrum.01845-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/19/2022] [Indexed: 11/20/2022] Open
Abstract
Listeria monocytogenes is a leading foodborne pathogen that can contaminate fresh produce in farm environment, resulting in deadly outbreaks. Composts contain a diversity of microorganisms, and some of them may be compost-adapted competitive exclusion microorganisms against L. monocytogenes. To understand interactions between compost microflora and the pathogen, both dairy- and poultry-wastes based composts (n = 12) were inoculated with L. monocytogenes, and then analyzed by next-generation sequencing approaches along with culturing methods. DNA extraction and enumeration of L. monocytogenes were performed at 0 and 72 h post-incubation at room temperature. The major bacterial phyla were identified as Firmicutes (23%), Proteobacteria (23%), Actinobacteria (19%), Chloroflexi (13%), Bacteroidetes (12%), Gemmatimonadetes (2%), and Acidobacteria (2%). The top three indicator genera enriched in different compost types were identified by LEfSe with LDA score > 2. The interactions between L. monocytogenes and indigenous microflora were limited as no significant changes in the dominant microbial members in compost ecosystem, but some discriminatory species such as Bacillus, Geobacillus, and Brevibacterium were identified by Random Forest analysis. Besides, changes in metabolic pathways and the increased abundance of bacteriocins category in the compost samples containing L. monocytogenes after 72 h postinoculation were revealed by metatranscriptomic sequencing. Taken together, the compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbial compositions, and the analysis of compost metagenome implied that interactions between L. monocytogenes and compost microflora may include competition for nutrients and the presence of antimicrobials. IMPORTANCE Listeria monocytogenes has been recognized as the etiological agent causing foodborne disease outbreaks, with fresh produce as vulnerable for contamination at even preharvest stage. Owing to the richness in microbial community, compost may mediate suppression of pathogens. In this study, the impact of compost-related factors and L. monocytogenes intrusion on dynamic changes in compost microbiome was investigated by next generation sequencing techniques. The compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbiome. The interactions between L. monocytogenes and compost microflora may include the competition for nutrients and the presence of antimicrobials produced by native compost microorganisms as potential competitive exclusion microorganisms. Findings from this study are important for the composting industry to understand the composition and functionality of microbial community in their products and help developing organic fertilizers fortified with anti-L. monocytogenes competitive exclusion microorganisms.
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Affiliation(s)
- Hongye Wang
- Department of Food, Nutrition, and Packaging Sciences, Clemson University, Clemson, South Carolina, USA
| | - Vijay Shankar
- Center for Human Genetics, Clemson University, Greenwood, South Carolina, USA
| | - Xiuping Jiang
- Department of Food, Nutrition, and Packaging Sciences, Clemson University, Clemson, South Carolina, USA
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45
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Trinh TND, Lee NY. Colorimetric detection of viable antibiotic resistant Enterococcus mediated by cordless operation of reverse transcription loop-mediated isothermal amplification. J Biotechnol 2022; 357:92-99. [PMID: 35952900 DOI: 10.1016/j.jbiotec.2022.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 07/12/2022] [Accepted: 08/05/2022] [Indexed: 11/20/2022]
Abstract
In this study, we applied a tube-based reverse transcription loop-mediated isothermal amplification technique using preloaded amplification and detection reagents for simple screening of viable vancomycin-resistant Enterococcus in a cordless manner. We adopted an mRNA-based approach to detect live Enterococcus in vancomycin-treated cultures. We used agarose to preload and store all reagents for amplification and detection inside the tube, which could achieve on-site isothermal nucleic acid amplification and detection in less than 1 h without using sophisticated instruments. Moreover, the use of a portable insulated water tumbler eliminated the need for electricity, which is usually important in nucleic acid amplification-based assays. The water tumbler acted as a heat source to supply a stable heat required for the amplification reaction, which could last up to 45 min. In addition, colorimetric detection was realized using pH-based methods. The detection was triggered by shaking the tube so that the amplified solution was reacted with phenolphthalein embedded in the tube cap. The introduced one-pot strategy has many advantages such as easy and cordless operation, low cost, disposability, and less chance of contamination because the amplification and detection occur in a closed system. The system could have a great impact on nucleic acid analyses in instrument-free and low-resource areas.
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Affiliation(s)
- Thi Ngoc Diep Trinh
- Department of Industrial Environmental Engineering, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, the Republic of Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do 13120, the Republic of Korea.
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46
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Guo J, Wang W, Zhao H, Luo Y, Wan M, Li Y. A new PMA-qPCR method for rapid and accurate detection of viable bacteria and spores of marine-derived Bacillus velezensis B-9987. J Microbiol Methods 2022; 199:106537. [DOI: 10.1016/j.mimet.2022.106537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 12/27/2022]
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Canh VD, Liu M, Sangsanont J, Katayama H. Capsid integrity detection of pathogenic viruses in waters: Recent progress and potential future applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154258. [PMID: 35248642 DOI: 10.1016/j.scitotenv.2022.154258] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/26/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Waterborne diseases caused by pathogenic human viruses are a major public health concern. To control the potential risk of viral infection through contaminated waters, a rapid, reliable tool to assess the infectivity of pathogenic viruses is required. Recently, an advanced approach (i.e., capsid integrity (RT-)qPCR) was developed to discriminate intact viruses (potentially infectious) from inactivated viruses. In this approach, samples were pretreated with capsid integrity reagents (e.g., monoazide dyes or metal compounds) before (RT -)qPCR. These reagents can only penetrate inactivated viruses with compromised capsids to bind to viral genomes and prevent their amplification, but they cannot enter viruses with intact capsids. Therefore, only viral genomes of intact viruses were amplified or detected by (RT-)qPCR after capsid integrity treatment. In this study, we reviewed recent progress in the development and application of capsid integrity (RT-)qPCR to assess the potential infectivity of viruses (including non-enveloped and enveloped viruses with different genome structures [RNA and DNA]) in water. The efficiency of capsid integrity (RT-)qPCR has been shown to depend on various factors, such as conditions of integrity reagent treatment, types of viruses, environmental matrices, and the capsid structure of viruses after disinfection treatments (e.g., UV, heat, and chlorine). For the application of capsid integrity (RT-)qPCR in real-world samples, the use of suitable virus concentration methods and process controls is important to control the efficiency of capsid integrity (RT-)qPCR. In addition, potential future applications of capsid integrity (RT-)qPCR for determining the mechanism of disinfection treatment on viral structure (e.g., capsid or genome) and a combination of capsid integrity treatment and next-generation sequencing (NGS) (capsid integrity NGS) for monitoring the community of intact pathogenic viruses in water are also discussed. This review provides essential information on the application of capsid integrity (RT-)qPCR as an efficient tool for monitoring the presence of pathogenic viruses with intact capsids in water.
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Affiliation(s)
- Vu Duc Canh
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Miaomiao Liu
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jatuwat Sangsanont
- Department of Environmental Science, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; Water Science and Technology for Sustainable Environmental Research Group, Chulalongkorn University, Bangkok 10330, Thailand
| | - Hiroyuki Katayama
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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48
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Wang H, Wagnon R, Moreno D, Timilsina S, Jones J, Vallad G, Turechek WW. A Long-Amplicon Viability-qPCR Test for Quantifying Living Pathogens that Cause Bacterial Spot in Tomato Seed. PLANT DISEASE 2022; 106:1474-1485. [PMID: 34894749 DOI: 10.1094/pdis-11-21-2509-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Bacterial spot is one of the most serious diseases of tomato. It is caused by four species of Xanthomonas: X. euvesicatoria, X. gardneri, X. perforans, and X. vesicatoria. Contaminated or infected seed can be a major source of inoculum for this disease. The use of certified pathogen-free seed is one of the primary management practices to reduce the inoculum load in commercial production. Current seed testing protocols rely mainly on plating the seed extract and conventional PCR; however, the plating method cannot detect viable but nonculturable cells, and the conventional PCR assay has limited capability to differentiate DNA extracted from viable or dead bacterial cells. To improve the sensitivity and specificity of the tomato seed testing method for bacterial spot pathogens, a long-amplicon quantitative PCR (qPCR) assay coupled with propidium monoazide (PMA-qPCR) was developed to quantify selectively the four pathogenic Xanthomonas species in tomato seed. The optimized PMA-qPCR procedure was evaluated on pure bacterial suspensions, bacteria-spiked seed extracts, and seed extracts of inoculated and naturally infected seed. A crude DNA extraction protocol also was developed, and PMA-qPCR with crude bacterial DNA extracts resulted in accurate quantification of 104 to 108 CFU/ml of viable bacteria when mixed with dead cells at concentrations as high as 107 CFU/ml in the seed extracts. With DNA purified from concentrated seed extracts, the PMA-qPCR assay was able to detect DNA of the target pathogens in seed samples spiked with ≥75 CFU/ml (about 0.5 CFU/seed) of the viable pathogens. Latent class analysis of the inoculated and naturally infected seed samples showed that the PMA-qPCR assay had greater sensitivity than plating the seed extracts on the semiselective modified Tween Medium B and CKTM media for all four target species. Being much faster and more sensitive than dilution plating, the PMA-qPCR assay has potential to be used as a standalone tool or in combination with the plating method to improve tomato seed testing and advance the production of clean seed.
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Affiliation(s)
- Hehe Wang
- EDISTO Research and Education Center, Clemson University, Blackville, SC 29817
| | - Rieanna Wagnon
- EDISTO Research and Education Center, Clemson University, Blackville, SC 29817
| | - Daniela Moreno
- EDISTO Research and Education Center, Clemson University, Blackville, SC 29817
| | | | | | - Gary Vallad
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598
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Daddy Gaoh S, Kweon O, Lee YJ, Hussong D, Marasa B, Ahn Y. A Propidium Monoazide (PMAxx)-Droplet Digital PCR (ddPCR) for the Detection of Viable Burkholderia cepacia Complex in Nuclease-Free Water and Antiseptics. Microorganisms 2022; 10:943. [PMID: 35630385 PMCID: PMC9147393 DOI: 10.3390/microorganisms10050943] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
Pharmaceutical products contaminated with Burkholderia cepacia complex (BCC) strains constitute a serious health issue for susceptible individuals. New detection methods to distinguish DNA from viable cells are required to ensure pharmaceutical product quality and safety. In this study, we have assessed a droplet digital PCR (ddPCR) with a variant propidium monoazide (PMAxx) for selective detection of live/dead BCC cells in autoclaved nuclease-free water after 365 days, in 0.001% chlorhexidine gluconate (CHX), and in 0.005% benzalkonium chloride (BZK) solutions after 184 days. Using 10 μM PMAxx and 5 min light exposure, a proportion of dead BCC was quantified by ddPCR. The detection limit of culture-based method was 104 CFU/mL, equivalent to 9.7 pg/μL for B. cenocepacia J2315, while that of ddPCR was 9.7 fg/μL. The true positive rate from nuclease-free water and CHX using PMAxx-ddPCR assay was 60.0% and 38.3%, respectively, compared to 85.0% and 74.6% without PMAxx (p < 0.05), respectively. However, in BZK-treated cells, no difference in the detection rate was observed between the ddPCR assay on samples treated with PMAxx (67.1%) and without PMAxx (63.3%). This study shows that the PMAxx-ddPCR assay provides a better tool for selective detection of live BCC cells in non-sterile pharmaceutical products.
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Affiliation(s)
- Soumana Daddy Gaoh
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (S.D.G.); (O.K.)
| | - Ohgew Kweon
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (S.D.G.); (O.K.)
| | - Yong-Jin Lee
- Department of Natural Sciences, Albany State University, Albany, GA 31705, USA;
| | - David Hussong
- Office of Pharmaceutical Science, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Beltsville, MD 20993, USA;
| | - Bernard Marasa
- Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA;
| | - Youngbeom Ahn
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (S.D.G.); (O.K.)
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50
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Hrdy J, Vasickova P. Virus detection methods for different kinds of food and water samples – The importance of molecular techniques. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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