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Djeghout B, Le-Viet T, Martins LDO, Savva GM, Evans R, Baker D, Page A, Elumogo N, Wain J, Janecko N. Capturing clinically relevant Campylobacter attributes through direct whole genome sequencing of stool. Microb Genom 2024; 10. [PMID: 39213166 DOI: 10.1099/mgen.0.001284] [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] [Indexed: 09/04/2024] Open
Abstract
Campylobacter is the leading bacterial cause of infectious intestinal disease, but the pathogen typically accounts for a very small proportion of the overall stool microbiome in each patient. Diagnosis is even more difficult due to the fastidious nature of Campylobacter in the laboratory setting. This has, in part, driven a change in recent years, from culture-based to rapid PCR-based diagnostic assays which have improved diagnostic detection, whilst creating a knowledge gap in our clinical and epidemiological understanding of Campylobacter genotypes - no isolates to sequence. In this study, direct metagenomic sequencing approaches were used to assess the possibility of replacing genome sequences with metagenome sequences; metagenomic sequencing outputs were used to describe clinically relevant attributes of Campylobacter genotypes. A total of 37 diarrhoeal stool samples with Campylobacter and five samples with an unknown pathogen result were collected and processed with and without filtration, DNA was extracted, and metagenomes were sequenced by short-read sequencing. Culture-based methods were used to validate Campylobacter metagenome-derived genome (MDG) results. Sequence output metrics were assessed for Campylobacter genome quality and accuracy of characterization. Of the 42 samples passing quality checks for analysis, identification of Campylobacter to the genus and species level was dependent on Campylobacter genome read count, coverage and genome completeness. A total of 65% (24/37) of samples were reliably identified to the genus level through Campylobacter MDG, 73% (27/37) by culture and 97% (36/37) by qPCR. The Campylobacter genomes with a genome completeness of over 60% (n=21) were all accurately identified at the species level (100%). Of those, 72% (15/21) were identified to sequence types (STs), and 95% (20/21) accurately identified antimicrobial resistance (AMR) gene determinants. Filtration of stool samples enhanced Campylobacter MDG recovery and genome quality metrics compared to the corresponding unfiltered samples, which improved the identification of STs and AMR profiles. The phylogenetic analysis in this study demonstrated the clustering of the metagenome-derived with culture-derived genomes and revealed the reliability of genomes from direct stool sequencing. Furthermore, Campylobacter genome spiking percentages ranging from 0 to 2% total metagenome abundance in the ONT MinION sequencer, configured to adaptive sequencing, exhibited better assembly quality and accurate identification of STs, particularly in the analysis of metagenomes containing 2 and 1% of Campylobacter jejuni genomes. Direct sequencing of Campylobacter from stool samples provides clinically relevant and epidemiologically important genomic information without the reliance on cultured genomes.
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Affiliation(s)
- Bilal Djeghout
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Thanh Le-Viet
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | | | - George M Savva
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Rhiannon Evans
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - David Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Andrew Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Ngozi Elumogo
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- Eastern Pathology Alliance, Norfolk and Norwich University Hospital, Norwich NR4 7UY, UK
| | - John Wain
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich NR4 7TJ, UK
| | - Nicol Janecko
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK
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2
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Rawindran H, Khoo KS, Ethiraj B, Lim JW, Liew CS, Goh PS, Raksasat R, Leong WH, Rajarathinam R, Ng HS, Tong WY, Alam MM. Environmental impact assessment via life cycle analysis on ultrafiltration membrane fabricated from polyethylene terephthalate waste to treat microalgal cultivation wastewater for reusability. ENVIRONMENTAL RESEARCH 2024; 251:118687. [PMID: 38493853 DOI: 10.1016/j.envres.2024.118687] [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: 10/22/2023] [Revised: 02/06/2024] [Accepted: 03/10/2024] [Indexed: 03/19/2024]
Abstract
The current study had conducted the life cycle analysis (LCA) to assess the environmental impact of microalgal wastewater treatment via an integrated membrane bioreactor. The functional unit selected for this analysis was 1 kg of treated microalgal wastewater with contaminants eliminated by ultrafiltration membrane fabricated from recycled polyethylene terephthalate waste. Meanwhile, the applied system boundary in this study was distinguished based on two scenarios, namely, cradle-to-gate encompassed wastewater treatment only and cradle-to-cradle which included the reutilization of treated wastewater to cultivate microalgae again. The environmental impacts and hotspots associated with the different stages of the wastewater treatment process had clearly elucidated that membrane treatment had ensued the highest impact, followed by microalgal harvesting, and finally cultivation. Among the environmental impact categories, water-related impact was found to be prominent in the following series: freshwater ecotoxicity, freshwater eutrophication and marine ecotoxicity. Notably, the key performance indicator of all environmental impact, i.e., the global warming potential was found to be very much lower at 2.94 × 10-4 kg CO2 eq as opposed to other literatures reported on the LCA of wastewater treatments using membranes. Overall, this study had proffered insights into the environmental impact of microalgal wastewater treatment and its stimulus for sustainable wastewater management. The findings of this study can be instrumental in making informed decision for optimizing microalgal wastewater treatment and reutilization assisted by membrane technology with an ultimate goal of enhancing sustainability.
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Affiliation(s)
- Hemamalini Rawindran
- Department of Chemistry, Faculty of Science, Centre for Sustainable Nanomaterials, Ibnu Sina Institute for Scientific and Industrial Research, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia.
| | - Kuan Shiong Khoo
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan
| | - Baranitharan Ethiraj
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Jun Wei Lim
- HICoE-Centre for Biofuel and Biochemical Research, Institute of Self-Sustainable Building, Department of Fundamental and Applied Sciences, Universiti Teknologi PETRONAS, 32610, Seri Iskandar, Perak Darul Ridzuan, Malaysia; Centre for Herbal Pharmacology and Environmental Sustainability, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, 603103, Tamil Nadu, India.
| | - Chin Seng Liew
- HICoE-Centre for Biofuel and Biochemical Research, Institute of Self-Sustainable Building, Department of Fundamental and Applied Sciences, Universiti Teknologi PETRONAS, 32610, Seri Iskandar, Perak Darul Ridzuan, Malaysia
| | - Pei Sean Goh
- Advanced Membrane Technology Research Centre, School of Chemical and Energy Engineering, Universiti Teknologi Malaysia, 81310, Johor, Malaysia
| | - Ratchaprapa Raksasat
- HICoE-Centre for Biofuel and Biochemical Research, Institute of Self-Sustainable Building, Department of Fundamental and Applied Sciences, Universiti Teknologi PETRONAS, 32610, Seri Iskandar, Perak Darul Ridzuan, Malaysia
| | - Wai Hong Leong
- Algal Bio Co. Ltd, Todai-Kashiwa Venture Plaza, 5-4-19 Kashiwanoha, Kashiwa, Chiba, 277-0082, Japan
| | - Ravikumar Rajarathinam
- Department of Biotechnology, Vel Tech Rangarajan Dr. Sagunthala R&D Institute of Science and Technology, Avadi, Chennai, 600062, India
| | - Hui-Suan Ng
- Department of Chemical and Materials Engineering, National Yunlin University of Science and Technology, 123 University Road, Section 3, Douliu, Yunlin 64002, Taiwan; College of Future, National Yunlin University of Science and Technology, 123 University Road, Section 3, Douliu, Yunlin 64002, Taiwan
| | - Woei-Yenn Tong
- Universiti Kuala Lumpur, Institute of Medical Science Technology, A1-1, Jalan TKS 1, Taman Kajang Sentral, 43000, Kajang, Selangor, Malaysia.
| | - Mohammad Mahtab Alam
- Department of Basic Medical Sciences, College of Applied Medical Science, King Khalid University, Abha, 61421, Saudi Arabia
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3
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Kokol V, Vivod V. Cation-exchange performance of a citric-acid esterified cellulose nanofibrous membrane for highly-selective proteins' permeability and adsorption capacity. Carbohydr Polym 2023; 318:121134. [PMID: 37479444 DOI: 10.1016/j.carbpol.2023.121134] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/01/2023] [Accepted: 06/16/2023] [Indexed: 07/23/2023]
Abstract
The usage of low-cost, readily available, or even disposable, single-use membranes in macromolecules' purification and separation is still in the development phase. In this research, highly porous (>95 %), water- and compression stable cation-exchange membranes were prepared by freeze-casting using cellulose nanofibrils (CNF) and citric acid (CA) acting as a crosslinker and source of weak anionic (carboxylic) surface groups arising from the mono-esterified CA. The membranes were characterized by different analytical techniques, and evaluated for the ionic adsorption efficacy of different proteins in dead-end filtration mode using a Tri-buffer of pH 8. The membrane's internal microstructure (porosity and density) with the available (quantity and access) carboxylic groups was confirmed, to determine not only the proteins' specific (related to the net charged and molecular weight) adsorption dynamic (>52 % of positive Lysozyme/Cytochrome, <8 % of negative BSA/Myoglobin; ≤0.5 g/L) at extremely high flow rates (>3.000 hL/h*MPa*m2), but also their desorption (>97 %) and re-equilibration (using NaCl) with flux recovery (>80 %). Such efficiency was achieved with up to 5 consecutive filtering cycles. The high permeability (>87 %) of the spherical and negatively surface charged microparticles (used as models) also suggests the likelihood of removing larger microbial species, which, while retaining relatively smaller and positively charged proteins, further increases their potential in biopharma applications.
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Affiliation(s)
- Vanja Kokol
- University of Maribor, Faculty of Mechanical Engineering, Institute of Engineering Materials and Design, Smetanova ulica 17, SI-2000 Maribor, Slovenia.
| | - Vera Vivod
- University of Maribor, Faculty of Mechanical Engineering, Institute of Engineering Materials and Design, Smetanova ulica 17, SI-2000 Maribor, Slovenia.
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4
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Kokol V, Kos M, Vivod V, Gunde-Cimerman N. Cationised Fibre-Based Cellulose Multi-Layer Membranes for Sterile and High-Flow Bacteria Retention and Inactivation. MEMBRANES 2023; 13:284. [PMID: 36984670 PMCID: PMC10059598 DOI: 10.3390/membranes13030284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Low-cost, readily available, or even disposable membranes in water purification or downstream biopharma processes are becoming attractive alternatives to expensive polymeric columns or filters. In this article, the potential of microfiltration membranes prepared from differently orientated viscose fibre slivers, infused with ultrafine quaternised (qCNF) and amino-hydrophobised (aCNF) cellulose nanofibrils, were investigated for capturing and deactivating the bacteria from water during vacuum filtration. The morphology and capturing mechanism of the single- and multi-layer structured membranes were evaluated using microscopic imaging and colloidal particles. They were assessed for antibacterial efficacy and the retention of selected bacterial species (Escherichia coli, Staphylococcus aureus, Micrococcus luteus), differing in the cell envelope structure, hydrodynamic biovolume (shape and size) and their clustering. The aCNF increased biocidal efficacy significantly when compared to qCNF-integrated membrane, although the latter retained bacteria equally effectively by a thicker multi-layer structured membrane. The retention of bacterial cells occurred through electrostatic and hydrophobic interactions, as well as via interfibrous pore diffusion, depending on their physicochemical properties. For all bacterial strains, the highest retention (up to 100% or log 6 reduction) at >50 L/h∗bar∗m2 flow rate was achieved with a 4-layer gradient-structured membrane containing different aCNF content, thereby matching the performance of industrial polymeric filters used for removing bacteria.
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Affiliation(s)
- Vanja Kokol
- Faculty of Mechanical Engineering, Institute of Engineering Materials and Design, University of Maribor, Smetanova 17, 2000 Maribor, Slovenia
| | - Monika Kos
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Vera Vivod
- Faculty of Mechanical Engineering, Institute of Engineering Materials and Design, University of Maribor, Smetanova 17, 2000 Maribor, Slovenia
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
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5
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Maini ZA, Lopez CM. Transitions in bacterial communities across two fermentation-based virgin coconut oil (VCO) production processes. Heliyon 2022; 8:e10154. [PMID: 36042721 PMCID: PMC9420384 DOI: 10.1016/j.heliyon.2022.e10154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/19/2022] [Accepted: 07/28/2022] [Indexed: 11/09/2022] Open
Abstract
Despite being one of the most used methods of virgin coconut oil (VCO) production, there is no metagenomic study that details the bacterial community shifts during fermentation-based VCO production. The identification and quantification of bacteria associated with coconut milk fermentation is useful for detecting the dominant microbial genera actively involved in VCO production which remains largely undescribed. Describing the constitutive microbial genera involved in this traditional fermentation practice can be used as a preliminary basis for improving industrial practices and developing better fermentation procedures. In this study, we utilized 16S rRNA metagenomic sequencing to trace the transitions in microbial community profiles as coconut milk is fermented to release VCO in two VCO production lines. The results show that difference in the microbiome composition between the different processing steps examined in this work was mainly due to the abundance of the Leuconostoc genus in the raw materials and its decline and transition into the lactic acid bacteria groups Weissella, Enterococcus, Lactobacillus, Lactococcus, and Streptococcus during the latter stages of fermentation. A total of 17 genera with relative abundances greater than 0.01% constitute the core microbiome of the two processing lines and account for 74%–97% of the microbial abundance in all coconut-derived samples. Significant correlations were shown through an analysis of the Spearman’s rank between and within the microbial composition and pH at the genus level. The results of the present study show that the dynamics of VCO fermentation rely on the shifts in abundances of various members of the Lactobacillales order.
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Affiliation(s)
- Zomesh A Maini
- Department of Biology, School of Science & Engineering, Loyola Schools, Ateneo de Manila University, Philippines
| | - Crisanto M Lopez
- Department of Biology, School of Science & Engineering, Loyola Schools, Ateneo de Manila University, Philippines
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6
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Zhang P, Kaushik AM, Mach KE, Hsieh K, Liao JC, Wang TH. Facile syringe filter-enabled bacteria separation, enrichment, and buffer exchange for clinical isolation-free digital detection and characterization of bacterial pathogens in urine. Analyst 2021; 146:2475-2483. [PMID: 33899069 PMCID: PMC10697054 DOI: 10.1039/d1an00039j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of accelerated methods for pathogen identification (ID) and antimicrobial susceptibility testing (AST) for infectious diseases is necessary to facilitate evidence-based antibiotic therapy and reduce clinical overreliance on broad-spectrum antibiotics. Towards this end, droplet-based microfluidics has unlocked remarkably rapid diagnostic assays with single-cell and single-molecule resolution. Yet, droplet platforms invariably rely on testing purified bacterial samples that have been clinically isolated after lengthy (>16 h) plating. While plating-based clinical isolation is important for enriching and separating out bacteria from background in clinical samples and also facilitating buffer exchange, it creates a diagnostic bottleneck that ultimately precludes droplet-based methods from achieving significantly accelerated times-to-result. To alleviate this bottleneck, we have developed facile syringe filter-enabled strategies for bacterial separation, enrichment, and buffer exchange from urine samples. By selecting appropriately sized filter membranes, we separated bacterial cells from background particulates in urine samples and achieved up to 91% bacterial recovery after such 1-step filtration. When interfaced with droplet-based detection of bacterial cells, 1-step filtration improved the limit of detection for bacterial ID and quantification by over an order of magnitude. We also developed a facile buffer exchange strategy to prepare bacteria in urine samples for droplet-based AST that achieved up to 10-fold bacterial enrichment during buffer exchange. Our filtration strategies, can be easily integrated into droplet workflows, enable clinical isolation-free sample-to-answer ID and AST, and significantly accelerate the turnaround of standard infectious disease diagnostic workflows.
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Affiliation(s)
- Pengfei Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Aniruddha M Kaushik
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. and Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
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7
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Fabrication, tuning and performance analysis of polyacrylonitrile (PAN)-derived microfiltration membranes for bacteria removal from drinking water. KOREAN J CHEM ENG 2021. [DOI: 10.1007/s11814-020-0666-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Li B, Sun D, Li B, Tang W, Ren P, Yu J, Zhang J. One-Step Electrochemically Prepared Graphene/Polyaniline Conductive Filter Membrane for Permeation Enhancement by Fouling Mitigation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:2209-2222. [PMID: 32050074 DOI: 10.1021/acs.langmuir.9b03114] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In the electrofiltration process, membrane conductivity plays a decisive role in improving the antifouling performance of the membrane. In this paper, combining the preparation of graphene (Gr) with the fabrication of the Gr layer on the surface of a polyaniline (PANI) membrane, a graphene/PANI (Gr/PANI) conductive membrane was prepared creatively by the one-step electrochemical method. The properties of the as-prepared Gr/PANI membrane were studied systematically. By the tests of Fourier transform infrared spectroscopy, Raman spectroscopy, X-ray diffraction, and atomic force microscopy, it was confirmed that Gr was successfully produced and was combined with the PANI membrane well. Field scanning electron microscopy with energy-dispersive X-ray analysis further confirmed that the top surface and the upper layer pore walls of the membrane were randomly covered by Gr. The antifouling performance of the prepared membrane was evaluated by studying the permeation flux of the yeast suspension, compared with the ones with no electric field: the total permeation flux at 1 V direct current (dc) increased by 109%; besides, under 1 V dc, the average flux of the Gr/PANI membrane was approximately 1.4 times that of the PANI membrane. This approach may provide a promising strategy for the combination of Gr with conductive polymers to produce separation membranes.
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Affiliation(s)
- Bojun Li
- Department of Chemical Engineering, Changchun University of Technology, 2055 Yanan Street, Changchun 130012, P. R. China
| | - De Sun
- Department of Chemical Engineering, Changchun University of Technology, 2055 Yanan Street, Changchun 130012, P. R. China
| | - Bingbing Li
- Department of Chemical Engineering, Changchun University of Technology, 2055 Yanan Street, Changchun 130012, P. R. China
| | - Wenjing Tang
- Department of Chemical Engineering, Changchun University of Technology, 2055 Yanan Street, Changchun 130012, P. R. China
| | - Ping Ren
- Department of Chemical Engineering, Changchun University of Technology, 2055 Yanan Street, Changchun 130012, P. R. China
| | - Jingtong Yu
- Department of Chemical Engineering, Changchun University of Technology, 2055 Yanan Street, Changchun 130012, P. R. China
| | - Jinhui Zhang
- Department of Chemical Engineering, Changchun University of Technology, 2055 Yanan Street, Changchun 130012, P. R. China
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9
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Ku S, Ximenes E, Kreke T, Foster K, Couetil JL, Zuponcic J, Zhao X, Hoagland L, Deering AJ, Ladisch MR. Microbial enrichment and multiplexed microfiltration for accelerated detection of Salmonella in spinach. Biotechnol Prog 2019; 35:e2874. [PMID: 31228331 DOI: 10.1002/btpr.2874] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/11/2019] [Accepted: 06/17/2019] [Indexed: 01/01/2023]
Abstract
To attain Salmonella detection thresholds in spinach suspensions using enrichment media requires at least 24 hr. Separation and concentration of selected microorganisms via microfiltration and microfugation reduce time for sample preparation, especially when working with large volumes of vegetable suspensions. This facilitates accelerated detection of Salmonella in spinach suspensions, and may contribute to effectively monitoring this pathogen before it reaches the consumer. We report a microfiltration-based protocol for accelerated sample preparation to concentrate and recover ≤1 colony forming unit (CFU) Salmonella/g pathogen-free spinach. Store-bought samples of spinach and a spinach plant subjected to two environmental conditions (temperature and light exposure) during its production were tested. The overall procedure involves extraction with buffer, a short enrichment step, prefiltration using a nylon filter, crossflow hollow fiber microfiltration, and retentate centrifugation to bring microbial cells to detection levels. Based on 1 CFU Salmonella/g frozen spinach, and a Poisson distribution statistical analyses with 99% probability, we calculated that 3 hr of incubation, when followed by microfiltration, is sufficient to reach the 2 log concentration required for Salmonella detection within 7 hr. Longer enrichment times (5 hr or more) is needed for concentrations lower than 1 CFU Salmonella/g of ready to eat spinach. The recovered microbial cells were identified and confirmed as Salmonella using both polymerase chain reaction (PCR) and plating methods. Different environmental conditions tested during production did not affect Salmonella viability; this demonstrated the broad adaptability of Salmonella and emphasized the need for methods that enable efficient monitoring of production for the presence of this pathogen.
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Affiliation(s)
- Seockmo Ku
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, Indiana
| | - Eduardo Ximenes
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, Indiana.,Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana
| | - Thomas Kreke
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, Indiana
| | - Kirk Foster
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | - Justin L Couetil
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, Indiana
| | - Jessica Zuponcic
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, Indiana.,Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana
| | - Xiaojun Zhao
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana
| | - Lori Hoagland
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana
| | - Amanda J Deering
- Department of Food Science, Purdue University, West Lafayette, Indiana
| | - Michael R Ladisch
- Laboratory of Renewable Resources Engineering, Purdue University, West Lafayette, Indiana.,Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana.,Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
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10
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Ou Y, Zhou D, Xu ZK, Wan LS. Surface modification of self-assembled isoporous polymer membranes for pressure-dependent high-resolution separation. Polym Chem 2019. [DOI: 10.1039/c9py00560a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Polymer membranes with narrow pore size distribution demonstrate great performance in high-resolution and high-efficiency separation.
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Affiliation(s)
- Yang Ou
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Key Laboratory of Adsorption and Separation Materials & Technologies of Zhejiang Province
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
| | - Di Zhou
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Key Laboratory of Adsorption and Separation Materials & Technologies of Zhejiang Province
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
| | - Zhi-Kang Xu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Key Laboratory of Adsorption and Separation Materials & Technologies of Zhejiang Province
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
| | - Ling-Shu Wan
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Key Laboratory of Adsorption and Separation Materials & Technologies of Zhejiang Province
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou 310027
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11
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Nnadozie CF, Lin J, Govinden R. Optimisation of protocol for effective detachment and selective recovery of the representative bacteria for extraction of metagenomic DNA from Eucalyptus spp. woodchips. J Microbiol Methods 2018; 148:155-160. [PMID: 29673787 DOI: 10.1016/j.mimet.2018.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
Abstract
For some environments such as planktonic/aqueous environments, the separation of bacteria cells from eukaryotic cells prior to DNA extraction using filtration is relatively straightforward. However, for woodchips, the bacteria are attached/embedded within the wood matrix, which prevents easy removal of bacterial cells. In this study, a method for the selective extraction of DNA from bacteria inhabiting Eucalyptus spp. woodchips has been developed. The objective was to compare milled and unmilled woodchips processed via three detachment methods, viz., sonication, vortexing and shaking followed by filtration using Teflon filters according to three relevant criteria: DNA yield, DNA purity and quality of DNA. Highest DNA yield was obtained by milling and vortexing for 10 min (77.50 ± 5.17 ng/μl), followed by milling and vortexing for 2 min (61.00 ± 6.56 ng/μl), unmilled and vortexing for 10 min (38.67 ± 5.17 ng/μl) and milled and shaking for 2 h (31.62 ± 5.17 ng/μl). The lowest DNA yield was obtained by using unmilled woodchips and 5 min of sonication treatment (7.00 ± 1.22 ng/μl). There was no significant difference in DNA purity for milled or unmilled woodchips processed via the three detachment methods. Duration of cell detachment treatment did not significantly influence DNA yield and purity. Following optimisation experiments, it was possible to extract bacterial DNA using milled woodchips and 10 minute vortexing devoid of DNA from the host background and other associated eukaryotes and of sufficient quality and quantity for metagenomic analysis.
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Affiliation(s)
- Chika F Nnadozie
- Biotechnology Cluster/Microbiology Discipline, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa.
| | - Johnson Lin
- Biotechnology Cluster/Microbiology Discipline, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa
| | - Roshini Govinden
- Biotechnology Cluster/Microbiology Discipline, School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban 4000, South Africa
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12
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Zheng H, Gao Y, Dong K, Hu N, Xu D, Hao M, Wu Z. A novel membrane-assisted fermentation coupling with foam separation for improving the titer of polymyxin E. SEP SCI TECHNOL 2017. [DOI: 10.1080/01496395.2017.1405984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Huijie Zheng
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, P.R. China
| | - Yingying Gao
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, P.R. China
| | - Kai Dong
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, P.R. China
| | - Nan Hu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, P.R. China
| | - Dandan Xu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, P.R. China
| | - Mengmeng Hao
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, P.R. China
| | - Zhaoliang Wu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, P.R. China
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13
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Ku S, Kreke T, Ximenes E, Foster K, Liu X, Gilpin CJ, Ladisch MR. Protein particulate retention and microorganism recovery for rapid detection of
Salmonella. Biotechnol Prog 2017; 33:687-695. [DOI: 10.1002/btpr.2468] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/22/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Seockmo Ku
- Laboratory of Renewable Resources EngineeringWest Lafayette IN47907‐2022
- Department of Agricultural and Biological EngineeringPurdue UniversityWest Lafayette IN47907‐2022
| | - Thomas Kreke
- Laboratory of Renewable Resources EngineeringWest Lafayette IN47907‐2022
| | - Eduardo Ximenes
- Laboratory of Renewable Resources EngineeringWest Lafayette IN47907‐2022
- Department of Agricultural and Biological EngineeringPurdue UniversityWest Lafayette IN47907‐2022
| | - Kirk Foster
- Weldon School of Biomedical EngineeringPurdue UniversityWest Lafayette IN47907‐2022
| | - Xingya Liu
- Laboratory of Renewable Resources EngineeringWest Lafayette IN47907‐2022
- Department of Agricultural and Biological EngineeringPurdue UniversityWest Lafayette IN47907‐2022
| | | | - Michael R. Ladisch
- Laboratory of Renewable Resources EngineeringWest Lafayette IN47907‐2022
- Department of Agricultural and Biological EngineeringPurdue UniversityWest Lafayette IN47907‐2022
- Weldon School of Biomedical EngineeringPurdue UniversityWest Lafayette IN47907‐2022
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14
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Gaveau A, Coetsier C, Roques C, Bacchin P, Dague E, Causserand C. Bacteria transfer by deformation through microfiltration membrane. J Memb Sci 2017. [DOI: 10.1016/j.memsci.2016.10.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Vibbert HB, Ku S, Li X, Liu X, Ximenes E, Kreke T, Ladisch MR, Deering AJ, Gehring AG. Accelerating sample preparation through enzyme-assisted microfiltration ofSalmonellain chicken extract. Biotechnol Prog 2015; 31:1551-62. [PMID: 26400739 DOI: 10.1002/btpr.2167] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/11/2015] [Indexed: 01/31/2023]
Affiliation(s)
- Hunter B. Vibbert
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Chemistry; Purdue University; West Lafayette IN 47907
| | - Seockmo Ku
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Agricultural and Biological Engineering; Purdue University; West Lafayette IN 47907
| | - Xuan Li
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Agricultural and Biological Engineering; Purdue University; West Lafayette IN 47907
| | - Xingya Liu
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Agricultural and Biological Engineering; Purdue University; West Lafayette IN 47907
| | - Eduardo Ximenes
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Agricultural and Biological Engineering; Purdue University; West Lafayette IN 47907
| | - Thomas Kreke
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Agricultural and Biological Engineering; Purdue University; West Lafayette IN 47907
- Weldon School of Biomedical Engineering; Purdue University; West Lafayette IN 47907
| | - Michael R. Ladisch
- Laboratory of Renewable Resources Engineering; Purdue University; West Lafayette IN 47907
- Dept. of Agricultural and Biological Engineering; Purdue University; West Lafayette IN 47907
- Weldon School of Biomedical Engineering; Purdue University; West Lafayette IN 47907
| | | | - Andrew G. Gehring
- US Department of Agriculture; Agricultural Research Service; Wyndmoor PA 19038
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