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Zhuang L, Gong J, Zhao Y, Yang J, Liu G, Zhao B, Song C, Zhang Y, Shen Q. Progress in methods for the detection of viable Escherichia coli. Analyst 2024; 149:1022-1049. [PMID: 38273740 DOI: 10.1039/d3an01750h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Escherichia coli (E. coli) is a prevalent enteric bacterium and a necessary organism to monitor for food safety and environmental purposes. Developing efficient and specific methods is critical for detecting and monitoring viable E. coli due to its high prevalence. Conventional culture methods are often laborious and time-consuming, and they offer limited capability in detecting potentially harmful viable but non-culturable E. coli in the tested sample, which highlights the need for improved approaches. Hence, there is a growing demand for accurate and sensitive methods to determine the presence of viable E. coli. This paper scrutinizes various methods for detecting viable E. coli, including culture-based methods, molecular methods that target DNAs and RNAs, bacteriophage-based methods, biosensors, and other emerging technologies. The review serves as a guide for researchers seeking additional methodological options and aiding in the development of rapid and precise assays. Moving forward, it is anticipated that methods for detecting E. coli will become more stable and robust, ultimately contributing significantly to the improvement of food safety and public health.
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Affiliation(s)
- Linlin Zhuang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 211102, P. R. China.
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, P. R. China
| | - Ying Zhao
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 211102, P. R. China.
| | - Jianbo Yang
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Guofang Liu
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Bin Zhao
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Chunlei Song
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
| | - Yu Zhang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Basic Medicine Research and Innovation Center of Ministry of Education, Zhongda Hospital, Southeast University, Nanjing 211102, P. R. China.
| | - Qiuping Shen
- School of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong 212400, P. R. China.
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Serghiou IR, Baker D, Evans R, Dalby MJ, Kiu R, Trampari E, Phillips S, Watt R, Atkinson T, Murphy B, Hall LJ, Webber MA. An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs. Microb Genom 2023; 9:mgen001058. [PMID: 37428148 PMCID: PMC10438817 DOI: 10.1099/mgen.0.001058] [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: 02/27/2023] [Accepted: 06/04/2023] [Indexed: 07/11/2023] Open
Abstract
The human skin microbiome represents a variety of complex microbial ecosystems that play a key role in host health. Molecular methods to study these communities have been developed but have been largely limited to low-throughput quantification and short amplicon-based sequencing, providing limited functional information about the communities present. Shotgun metagenomic sequencing has emerged as a preferred method for microbiome studies as it provides more comprehensive information about the species/strains present in a niche and the genes they encode. However, the relatively low bacterial biomass of skin, in comparison to other areas such as the gut microbiome, makes obtaining sufficient DNA for shotgun metagenomic sequencing challenging. Here we describe an optimised high-throughput method for extraction of high molecular weight DNA suitable for shotgun metagenomic sequencing. We validated the performance of the extraction method, and analysis pipeline on skin swabs collected from both adults and babies. The pipeline effectively characterised the bacterial skin microbiota with a cost and throughput suitable for larger longitudinal sets of samples. Application of this method will allow greater insights into community compositions and functional capabilities of the skin microbiome.
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Affiliation(s)
- Iliana R. Serghiou
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Dave Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Rhiannon Evans
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Matthew J. Dalby
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Raymond Kiu
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Eleftheria Trampari
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Sarah Phillips
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Rachel Watt
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Thomas Atkinson
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Barry Murphy
- Unilever R&D Port Sunlight, Bebington, CH63 3JW, UK
| | - Lindsay J. Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Mark A. Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
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Tao W, Song Y, Singhal N, McGoverin C, Vanholsbeeck F, Swift S. A novel optical biosensor for in situ and small-scale monitoring of bacterial transport in saturated columns. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 289:112452. [PMID: 33813297 DOI: 10.1016/j.jenvman.2021.112452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 03/05/2021] [Accepted: 03/17/2021] [Indexed: 06/12/2023]
Abstract
In situ monitoring techniques can provide new insight into bacterial transport after inoculating exogenous bacteria into contaminated soils for bioremediation. A real-time and non-destructive optical sensor (the optrode) was employed to monitor in situ transport of two fluorescently labelled bacteria - Green Fluorescent Protein (Gfp)-labelled, hydrophilic Pseudomonas putida and Tomato Fluorescent Protein (td)-labelled, hydrophobic Rhodococcus erythropolis, in a saturated sand column with and without rhamnolipid surfactant. In situ measurements were made at three sampling ports in the column with the optrode in two sets of column experiments. In Experiment 1, liquid samples were extracted for ex situ analyses (plate counts and fluorescence), while in Experiment 2 no liquid samples were extracted. Extracting liquid samples for ex situ analyses in Experiment 1 disturbed in situ measurements; in situ measured bacterial concentrations were lower, or a significant lag in breakthrough occurred relative to ex situ measurements. In Experiment 2, the optrode worked well in monitoring bacterial transport, which gave consistent transport parameters at each sampling port. Moreover, the optrode enabled the impact of bacterial hydrophobicity and rhamnolipid surfactant on bacterial transport to be observed. Specifically, hydrophilic P. putida was transported faster through the column than hydrophobic R. erythropolis; we infer from this result that fewer P. putida cells adsorb to sand particles than do R. erythropolis cells. The rhamnolipid surfactant enhanced the transport of both hydrophilic and hydrophobic bacteria. These two observations are consistent with Lifshitz-van der Waals forces and acid-base interactions between bacteria and sand.
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Affiliation(s)
- Wei Tao
- School of Chemistry and Environmental Engineering, Sichuan University of Science and Engineering, Zigong, 643000, PR China; Department of Civil and Environmental Engineering, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Yantao Song
- Department of Civil and Environmental Engineering, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Naresh Singhal
- Department of Civil and Environmental Engineering, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Cushla McGoverin
- The Dodds-Walls Centre for Photonic and Quantum Technologies, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand; Department of Physics, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Frédérique Vanholsbeeck
- The Dodds-Walls Centre for Photonic and Quantum Technologies, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand; Department of Physics, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand
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Monitoring of transfer and internalization of Escherichia coli from inoculated knives to fresh cut cucumbers (Cucumis sativus L.) using bioluminescence imaging. Sci Rep 2021; 11:11425. [PMID: 34075080 PMCID: PMC8169731 DOI: 10.1038/s41598-021-90584-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/14/2021] [Indexed: 11/19/2022] Open
Abstract
Slicing may cause the risk of cross-contamination in cucumber. In this study, knife inoculated with Escherichia coli (E. coli) was used to cut cucumbers, bioluminescence imaging (BLI) was used to visualize the possible distribution and internalization of E. coli during cutting and storage. Results showed that the initial two slices resulted in greater bacterial transfer. The bacterial transfer exhibited a fluctuating decay trend, E. coli was most distributed at the initial cutting site. The contaminated area on the surface of cucumber slices decreased during the storage period, which can be attributed to the death and internalization of E. coli. The maximum internalization distance of E. coli was about 2–3 mm, and did not further spread after 30 min from inoculation. Hence, our results provide useful information for risk management in both home and industrial environment.
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Comparison of Preservation Methods of Staphylococcus aureus and Escherichia coli Bacteria. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.3.58] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the most important problems faced by microbiologists is to preserve bacterial isolates in the best state to study and further diagnosis. The current study aims to provide a summary of experimental results to maintain two species of bacteria alive after being stored by using some additives. This study found that the best temperature to preserve Staphylococcus aureus was -20°C for a year, while for Escherichia coli it was the same temperature except in using Glycerol (G) 100% and Food oil (FO) methods. The optimum method to preserve S. aureus was by using Normal Saline (NS), while Distilled Water (DW) was the optimum method to preserve E. coli at temperatures (4, 25 and -20)°C for a year, the phenotypic patterns for examining bacteria were maintained except in NS at 4°C for S. aureus after a year ago. Glycerol was used alone at concentrations (100, 50, 30 and 15)%, and another group used G+NS in the same volumes, good results were achieved when it used alone or with NS to preserve bacteria for six months at 4°C except for methods of G100% and (G100% + NS) for examining bacteria. FO has never been used as preservation liquid, it is successful to survive S. aureus at -20°C for a year, and when it was added to NS, E. coli survived for a year at three temperatures (4, 25 and -20)°C, while S. aureus didn’t survive for a year when FO+NS method used at room temperature. The precipitation method was used for bacterial suspension, then added the preserving liquid, but the results were not effective compared to the First method.
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6
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Bandy AM, Cook K, Fryar AE, Zhu J. Differential Transport of Escherichia coli Isolates Compared to Abiotic Tracers in a Karst Aquifer. GROUND WATER 2020; 58:70-78. [PMID: 30982960 DOI: 10.1111/gwat.12889] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Lack of filtration and rapid transport of groundwater and particulate matter make karst aquifers susceptible to bacterial contamination. This study utilized quantitative polymerase chain reaction (qPCR) to examine the transport and attenuation of two nonvirulent isolates of Escherichia coli (E. coli) in relation to traditional groundwater tracers (rhodamine WT dye and 1-µm diameter latex microspheres) in a karst-conduit aquifer in central Kentucky. Bacterial isolates were labeled with stable isotopes (15 N and 13 C). All tracers were detected more than 6 km downstream from the injection site and demonstrated overlapping breakthrough curves, with differential transport observed between the two bacterial strains. The E. coli isolate containing the kps gene (low attachment) arrived at sampling sites 1.25 to 36 h prior to the bacterial isolate containing the iha gene (high attachment) and was detected in samples collected following storm events in which the iha isolate was not detected. The storage potential of contaminants within karst systems was demonstrated by the remobilization of all tracers during storm events more than 1 month after injection. Bacteria-sized microspheres were more easily remobilized during periods of increased discharge compared to other tracers. The study demonstrated that molecular biology techniques such as qPCR can be utilized as a sensitive analysis of bacterial tracers in karst aquifers and may prove to be a more sensitive analytical technique than stable isotope analysis for field-scale traces.
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Affiliation(s)
| | - Kimberly Cook
- USDA Agricultural Research Service, Bacterial Epidemiology and Antimicrobial Resistance Research Unit, U.S. National Poultry Research Center, 950 College Station Rd, Athens, GA, 30605
| | - Alan E Fryar
- Department of Earth and Environmental Sciences, University of Kentucky, 101 Slone Research Bldg., Lexington, KY, 40506-0053
| | - Junfeng Zhu
- Kentucky Geological Survey, University of Kentucky, 228 Mining and Mineral Resources Bldg., Lexington, KY, 40506-0107
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Alegbeleye OO, Singleton I, Sant'Ana AS. Sources and contamination routes of microbial pathogens to fresh produce during field cultivation: A review. Food Microbiol 2018; 73:177-208. [PMID: 29526204 PMCID: PMC7127387 DOI: 10.1016/j.fm.2018.01.003] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/31/2017] [Accepted: 01/02/2018] [Indexed: 12/17/2022]
Abstract
Foodborne illness resulting from the consumption of contaminated fresh produce is a common phenomenon and has severe effects on human health together with severe economic and social impacts. The implications of foodborne diseases associated with fresh produce have urged research into the numerous ways and mechanisms through which pathogens may gain access to produce, thereby compromising microbiological safety. This review provides a background on the various sources and pathways through which pathogenic bacteria contaminate fresh produce; the survival and proliferation of pathogens on fresh produce while growing and potential methods to reduce microbial contamination before harvest. Some of the established bacterial contamination sources include contaminated manure, irrigation water, soil, livestock/ wildlife, and numerous factors influence the incidence, fate, transport, survival and proliferation of pathogens in the wide variety of sources where they are found. Once pathogenic bacteria have been introduced into the growing environment, they can colonize and persist on fresh produce using a variety of mechanisms. Overall, microbiological hazards are significant; therefore, ways to reduce sources of contamination and a deeper understanding of pathogen survival and growth on fresh produce in the field are required to reduce risk to human health and the associated economic consequences.
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Affiliation(s)
| | - Ian Singleton
- School of Applied Sciences, Sighthill Campus, Edinburgh Napier University, Edinburgh, UK
| | - Anderson S Sant'Ana
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil.
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8
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Alimohammadi F, Sharifian Gh M, Attanayake NH, Thenuwara AC, Gogotsi Y, Anasori B, Strongin DR. Antimicrobial Properties of 2D MnO 2 and MoS 2 Nanomaterials Vertically Aligned on Graphene Materials and Ti 3C 2 MXene. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:7192-7200. [PMID: 29782792 DOI: 10.1021/acs.langmuir.8b00262] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Two-dimensional (2D) nanomaterials have attracted considerable attention in biomedical and environmental applications due to their antimicrobial activity. In the interest of investigating the primary antimicrobial mode-of-action of 2D nanomaterials, we studied the antimicrobial properties of MnO2 and MoS2, toward Gram-positive and Gram-negative bacteria. Bacillus subtilis and Escherichia coli bacteria were treated individually with 100 μg/mL of randomly oriented and vertically aligned nanomaterials for ∼3 h in the dark. The vertically aligned 2D MnO2 and MoS2 were grown on 2D sheets of graphene oxide, reduced graphene oxide, and Ti3C2 MXene. Measurements to determine the viability of bacteria in the presence of the 2D nanomaterials performed by using two complementary techniques, flow cytometry, and fluorescence imaging showed that, while MnO2 and MoS2 nanosheets show different antibacterial activities, in both cases, Gram-positive bacteria show a higher loss in membrane integrity. Scanning electron microscopy images suggest that the 2D nanomaterials, which have a detrimental effect on bacteria viability, compromise the cell wall, leading to significant morphological changes. We propose that the peptidoglycan mesh (PM) in the bacterial wall is likely the primary target of the 2D nanomaterials. Vertically aligned 2D MnO2 nanosheets showed the highest antimicrobial activity, suggesting that the edges of the nanosheets were likely compromising the cell walls upon contact.
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Affiliation(s)
- Farbod Alimohammadi
- Department of Chemistry , Temple University , 1901 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
- Center for Computational Design of Functional Layered Materials (CCDM) , Temple University , 1925 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Mohammad Sharifian Gh
- Department of Chemistry , Temple University , 1901 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Nuwan H Attanayake
- Department of Chemistry , Temple University , 1901 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
- Center for Computational Design of Functional Layered Materials (CCDM) , Temple University , 1925 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Akila C Thenuwara
- Department of Chemistry , Temple University , 1901 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
- Center for Computational Design of Functional Layered Materials (CCDM) , Temple University , 1925 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
| | - Yury Gogotsi
- Department of Materials Science and Engineering, and A. J. Drexel Nanomaterials Institute , Drexel University , Philadelphia , Pennsylvania 19104 , United States
| | - Babak Anasori
- Department of Materials Science and Engineering, and A. J. Drexel Nanomaterials Institute , Drexel University , Philadelphia , Pennsylvania 19104 , United States
| | - Daniel R Strongin
- Department of Chemistry , Temple University , 1901 North 13th Street , Philadelphia , Pennsylvania 19122 , United States
- Center for Computational Design of Functional Layered Materials (CCDM) , Temple University , 1925 North 12th Street , Philadelphia , Pennsylvania 19122 , United States
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9
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Bandy A, Cook K, Fryar AE, Polk J. Use of Molecular Markers to Compare Escherichia coli Transport with Traditional Groundwater Tracers in Epikarst. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:88-95. [PMID: 29415110 DOI: 10.2134/jeq2017.10.0406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bacterial contamination of karst aquifers is a global concern as water quality deteriorates in the face of decreasing water security. Traditional abiotic groundwater tracers, which do not exhibit surface properties similar to bacteria, may not be good proxies for risk assessment of bacterial transport in karst environments. This study examined the transport and attenuation of two isolates of in relation to traditional groundwater tracers (rhodamine WT dye and 1-μm-diam. latex microspheres) through ∼30 m of epikarst in western Kentucky. Differential movement of the four tracers was observed, with tracer behavior dependent on flow conditions. Dye arrived at the sampling site prior to particulates. Molecular biology techniques successfully detected bacteria in the cave and showed attenuation was greater for a bacterial isolate with high attachment efficiency compared with an isolate known to have low attachment efficiency. Microspheres were first detected simultaneously with the low-attachment isolate but attained maximum concentrations during increases in discharge >11 d post-injection. Bacteria were remobilized by storm events >60 d after injection, illustrating the storage capacity of epikarst with regard to potential contaminants. The two bacterial strains were not transported at the same rate within the epikarst, showing breakthroughs during differing storm events and illustrating the importance of cell surface chemistry in the prediction of microorganism movement. Moreover, this study has shown that molecular analysis can be successfully used to target, quantify, and track introduced microbial tracers in karst terrains.
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Hassard F, Gwyther CL, Farkas K, Andrews A, Jones V, Cox B, Brett H, Jones DL, McDonald JE, Malham SK. Abundance and Distribution of Enteric Bacteria and Viruses in Coastal and Estuarine Sediments-a Review. Front Microbiol 2016; 7:1692. [PMID: 27847499 PMCID: PMC5088438 DOI: 10.3389/fmicb.2016.01692] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/10/2016] [Indexed: 11/26/2022] Open
Abstract
The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically <10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.
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Affiliation(s)
| | - Ceri L. Gwyther
- Department of Engineering and Innovation, Open UniversityMilton Keynes, UK
| | - Kata Farkas
- School of Environment, Natural Resources and Geography, Bangor UniversityBangor, UK
| | | | | | | | | | - Davey L. Jones
- School of Environment, Natural Resources and Geography, Bangor UniversityBangor, UK
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11
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Gomes IB, Simões M, Simões LC. The effects of sodium hypochlorite against selected drinking water-isolated bacteria in planktonic and sessile states. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 565:40-48. [PMID: 27156214 DOI: 10.1016/j.scitotenv.2016.04.136] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/16/2016] [Accepted: 04/17/2016] [Indexed: 06/05/2023]
Affiliation(s)
- I B Gomes
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal.
| | - M Simões
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465 Porto, Portugal.
| | - L C Simões
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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12
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Shahrokh Esfahani S, Emtiazi G, Shafiei R, Ghorbani N, Zarkesh Esfahani SH. Tolerance Induction of Temperature and Starvation with Tricalcium Phosphate on Preservation and Sporulation in Bacillus amyloliquefaciens Detected by Flow Cytometry. Curr Microbiol 2016; 73:366-373. [DOI: 10.1007/s00284-016-1066-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/13/2016] [Indexed: 11/24/2022]
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13
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Ray JCJ, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G. Cellular Growth Arrest and Persistence from Enzyme Saturation. PLoS Comput Biol 2016; 12:e1004825. [PMID: 27010473 PMCID: PMC4820279 DOI: 10.1371/journal.pcbi.1004825] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 02/22/2016] [Indexed: 11/18/2022] Open
Abstract
Metabolic efficiency depends on the balance between supply and demand of metabolites, which is sensitive to environmental and physiological fluctuations, or noise, causing shortages or surpluses in the metabolic pipeline. How cells can reliably optimize biomass production in the presence of metabolic fluctuations is a fundamental question that has not been fully answered. Here we use mathematical models to predict that enzyme saturation creates distinct regimes of cellular growth, including a phase of growth arrest resulting from toxicity of the metabolic process. Noise can drive entry of single cells into growth arrest while a fast-growing majority sustains the population. We confirmed these predictions by measuring the growth dynamics of Escherichia coli utilizing lactose as a sole carbon source. The predicted heterogeneous growth emerged at high lactose concentrations, and was associated with cell death and production of antibiotic-tolerant persister cells. These results suggest how metabolic networks may balance costs and benefits, with important implications for drug tolerance. In bacteria, changes in gene expression, with resulting changes in protein concentration, can drastically change how fast cells and cellular populations grow. This fact has big implications for how we treat infectious disease, which types of organisms make up our microbiomes, and what patterns of gene regulation have undergone evolutionary selection. Here, we show how, in principle, the expression level of a single enzyme can affect bacterial population growth by creating a threshold where cells grow optimally fast just below it, but rapidly reach a state of no growth just above it because metabolic byproducts build up and halt growth. The narrow margin between these two states makes entering either of them possible for the same bacterium because of intrinsic uncertainty, or "noise", in gene expression. The predicted result is a variety of growth rates in a single population of genetically identical cells, manifested as a mix of fast- and slow-growing cells. We created laboratory conditions that reproduce the effect in the model organism E. coli, and showed that there may be a benefit to having slower growing cells, because they can survive antibiotic exposure for longer.
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Affiliation(s)
- J Christian J Ray
- The University of Texas MD Anderson Cancer Center, Department of Systems Biology, Houston, Texas, United States of America.,Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America.,Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Michelle L Wickersheim
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Ameya P Jalihal
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America.,SASTRA University, Tirumalaisamudram, Tamil Nadu, India
| | - Yusuf O Adeshina
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Tim F Cooper
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Gábor Balázsi
- The University of Texas MD Anderson Cancer Center, Department of Systems Biology, Houston, Texas, United States of America.,Laufer Center for Physical & Quantitative Biology and Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, United States of America
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Malheiro J, Araújo P, Machado I, Lemos M, Mergulhão F, Melo L, Simões M. The Effects of Selected Brominated and Chlorinated Chemicals onPseudomonas fluorescensPlanktonic Cells and Flow-Generated Biofilms. J FOOD PROCESS PRES 2015. [DOI: 10.1111/jfpp.12609] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- J. Malheiro
- LEPABE; Department of Chemical Engineering; Faculty of Engineering; University of Porto; Rua Dr. Roberto Frias s/n 4200-465 Porto Portugal
| | - P. Araújo
- LEPABE; Department of Chemical Engineering; Faculty of Engineering; University of Porto; Rua Dr. Roberto Frias s/n 4200-465 Porto Portugal
| | - I. Machado
- LEPABE; Department of Chemical Engineering; Faculty of Engineering; University of Porto; Rua Dr. Roberto Frias s/n 4200-465 Porto Portugal
| | - M. Lemos
- LEPABE; Department of Chemical Engineering; Faculty of Engineering; University of Porto; Rua Dr. Roberto Frias s/n 4200-465 Porto Portugal
- Department of Chemical Engineering & Biotechnology; New Museums Site; Cambridge UK
| | - F. Mergulhão
- LEPABE; Department of Chemical Engineering; Faculty of Engineering; University of Porto; Rua Dr. Roberto Frias s/n 4200-465 Porto Portugal
| | - L. Melo
- LEPABE; Department of Chemical Engineering; Faculty of Engineering; University of Porto; Rua Dr. Roberto Frias s/n 4200-465 Porto Portugal
| | - M. Simões
- LEPABE; Department of Chemical Engineering; Faculty of Engineering; University of Porto; Rua Dr. Roberto Frias s/n 4200-465 Porto Portugal
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15
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Bacterial Cyanuric Acid Hydrolase for Water Treatment. Appl Environ Microbiol 2015; 81:6660-8. [PMID: 26187963 DOI: 10.1128/aem.02175-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 07/10/2015] [Indexed: 11/20/2022] Open
Abstract
Di- and trichloroisocyanuric acids are widely used as water disinfection agents, but cyanuric acid accumulates with repeated additions and must be removed to maintain free hypochlorite for disinfection. This study describes the development of methods for using a cyanuric acid-degrading enzyme contained within nonliving cells that were encapsulated within a porous silica matrix. Initially, three different bacterial cyanuric acid hydrolases were compared: TrzD from Acidovorax citrulli strain 12227, AtzD from Pseudomonas sp. strain ADP, and CAH from Moorella thermoacetica ATCC 39073. Each enzyme was expressed recombinantly in Escherichia coli and tested for cyanuric acid hydrolase activity using freely suspended or encapsulated cell formats. Cyanuric acid hydrolase activities differed by only a 2-fold range when comparing across the different enzymes with a given format. A practical water filtration system is most likely to be used with nonviable cells, and all cells were rendered nonviable by heat treatment at 70°C for 1 h. Only the CAH enzyme from the thermophile M. thermoacetica retained significant activity under those conditions, and so it was tested in a flowthrough system simulating a bioreactive pool filter. Starting with a cyanuric acid concentration of 10,000 μM, more than 70% of the cyanuric acid was degraded in 24 h, it was completely removed in 72 h, and a respike of 10,000 μM cyanuric acid a week later showed identical biodegradation kinetics. An experiment conducted with water obtained from municipal swimming pools showed the efficacy of the process, although cyanuric acid degradation rates decreased by 50% in the presence of 4.5 ppm hypochlorite. In total, these experiments demonstrated significant robustness of cyanuric acid hydrolase and the silica bead materials in remediation.
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16
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Ebner P, Prax M, Nega M, Koch I, Dube L, Yu W, Rinker J, Popella P, Flötenmeyer M, Götz F. Excretion of cytoplasmic proteins (ECP) inStaphylococcus aureus. Mol Microbiol 2015; 97:775-89. [DOI: 10.1111/mmi.13065] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Patrick Ebner
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine (IMIT); University of Tübingen; Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Marcel Prax
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine (IMIT); University of Tübingen; Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Mulugeta Nega
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine (IMIT); University of Tübingen; Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Iris Koch
- Max Planck Institute for Developmental Biology; Spemannstr. 35 72076 Tübingen Germany
| | - Linda Dube
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine (IMIT); University of Tübingen; Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Wenqi Yu
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine (IMIT); University of Tübingen; Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Janina Rinker
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine (IMIT); University of Tübingen; Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Peter Popella
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine (IMIT); University of Tübingen; Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Matthias Flötenmeyer
- Max Planck Institute for Developmental Biology; Spemannstr. 35 72076 Tübingen Germany
| | - Friedrich Götz
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine (IMIT); University of Tübingen; Auf der Morgenstelle 28 72076 Tübingen Germany
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17
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Spatial and temporal features of the growth of a bacterial species colonizing the zebrafish gut. mBio 2014; 5:mBio.01751-14. [PMID: 25516613 PMCID: PMC4271548 DOI: 10.1128/mbio.01751-14] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The vertebrate intestine is home to microbial ecosystems that play key roles in host development and health. Little is known about the spatial and temporal dynamics of these microbial communities, limiting our understanding of fundamental properties, such as their mechanisms of growth, propagation, and persistence. To address this, we inoculated initially germ-free zebrafish larvae with fluorescently labeled strains of an Aeromonas species, representing an abundant genus in the zebrafish gut. Using light sheet fluorescence microscopy to obtain three-dimensional images spanning the gut, we quantified the entire bacterial load, as founding populations grew from tens to tens of thousands of cells over several hours. The data yield the first ever measurements of the growth kinetics of a microbial species inside a live vertebrate intestine and show dynamics that robustly fit a logistic growth model. Intriguingly, bacteria were nonuniformly distributed throughout the gut, and bacterial aggregates showed considerably higher growth rates than did discrete individuals. The form of aggregate growth indicates intrinsically higher division rates for clustered bacteria, rather than surface-mediated agglomeration onto clusters. Thus, the spatial organization of gut bacteria both relative to the host and to each other impacts overall growth kinetics, suggesting that spatial characterizations will be an important input to predictive models of host-associated microbial community assembly. Our intestines are home to vast numbers of microbes that influence many aspects of health and disease. Though we now know a great deal about the constituents of the gut microbiota, we understand very little about their spatial structure and temporal dynamics in humans or in any animal: how microbial populations establish themselves, grow, fluctuate, and persist. To address this, we made use of a model organism, the zebrafish, and a new optical imaging technique, light sheet fluorescence microscopy, to visualize for the first time the colonization of a live, vertebrate gut by specific bacteria with sufficient resolution to quantify the population over a range from a few individuals to tens of thousands of bacterial cells. Our results provide unprecedented measures of bacterial growth kinetics and also show the influence of spatial structure on bacterial populations, which can be revealed only by direct imaging.
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18
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Liu P, Wu X, Liao C, Liu X, Du J, Shi H, Wang X, Bai X, Peng P, Yu L, Wang F, Zhao Y, Liu M. Escherichia coli and Candida albicans induced macrophage extracellular trap-like structures with limited microbicidal activity. PLoS One 2014; 9:e90042. [PMID: 24587206 PMCID: PMC3934966 DOI: 10.1371/journal.pone.0090042] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 01/27/2014] [Indexed: 01/21/2023] Open
Abstract
The formation of extracellular traps (ETs) has recently been recognized as a novel defense mechanism in several types of innate immune cells. It has been suggested that these structures are toxic to microbes and contribute significantly to killing several pathogens. However, the role of ETs formed by macrophages (METs) in defense against microbes remains little known. In this study, we demonstrated that a subset of murine J774A.1 macrophage cell line (8% to 17%) and peritoneal macrophages (8.5% to 15%) form METs-like structures (METs-LS) in response to Escherichia coli and Candida albicans challenge. We found only a portion of murine METs-LS, which are released by dying macrophages, showed detectable killing effects on trapped E. coli but not C. albicans. Fluorescence and scanning electron microscopy analyses revealed that, in vitro, both microorganisms were entrapped in J774A.1 METs-LS composed of DNA and microbicidal proteins such as histone, myeloperoxidase and lysozyme. DNA components of both nucleus and mitochondrion origins were detectable in these structures. Additionally, METs-LS formation occurred independently of ROS produced by NADPH oxidase, and this process did not result in cell lysis. In summary, our results emphasized that microbes induced METs-LS in murine macrophage cells and that the microbicidal activity of these METs-LS differs greatly. We propose the function of METs-LS is to contain invading microbes at the infection site, thereby preventing the systemic diffusion of them, rather than significantly killing them.
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Affiliation(s)
- Pan Liu
- Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Xiuping Wu
- Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Chengshui Liao
- Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Xiaolei Liu
- Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Jing Du
- Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Haining Shi
- Mucosal Immunology Laboratory, Pediatric Gastroenterology Unit, Massachusetts General Hospital East, Charlestown, Massachusetts, United States of America
| | - Xuelin Wang
- Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Xue Bai
- Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Peng Peng
- Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Lu Yu
- Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Feng Wang
- Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Ying Zhao
- Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
| | - Mingyuan Liu
- Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, Jilin University, Changchun, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- * E-mail:
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Santos CM, Kumar A, Kolar SS, Contreras-Caceres R, McDermott A, Cai C. Immobilization of antimicrobial peptide IG-25 onto fluoropolymers via fluorous interactions and click chemistry. ACS APPLIED MATERIALS & INTERFACES 2013; 5:12789-93. [PMID: 24266746 PMCID: PMC3925349 DOI: 10.1021/am404591n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We report a practical method for biofunctionalization of fluoropolymers based on noncovalent, fluorous interactions and click chemistry that allows incorporation of biomolecules under physiological solutions. We demonstrate the method by immobilization of an antimicrobial peptide (AMP) on fluorous thin films and fluorosilicone contact lens. The fluorous surfaces were dip-coated with fluorous-tagged oligo(ethylene) chain terminated with a reactive group, such as an alkynyl group. This simple step generates a "clickable" surface. The noncovalent fluorous interaction was strong enough to allow subsequent covalent attachment of IG-25, a truncated version of the most extensively studied human AMP LL-37. The attachment was through copper-catalyzed click reaction between the alkynyl group on the surface and the azido-OEG tag at the N-terminus of IG-25. In comparison to surfaces presenting IG-25 randomly bound via carbodiimide chemistry, the surfaces presenting IG-25 tethering to the surface at the N-terminus via click chemistry displayed higher antibacterial activities against an ocular pathogen Pseudomonas aeruginosa (strain PA-O1).
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Affiliation(s)
| | - Amit Kumar
- Department of Chemistry, University of Houston, Houston, Texas 77204, USA
| | - Satya S. Kolar
- College of Optometry, University of Houston, Houston, Texas 77204, USA
| | | | - Alison McDermott
- College of Optometry, University of Houston, Houston, Texas 77204, USA
| | - Chengzhi Cai
- Department of Chemistry, University of Houston, Houston, Texas 77204, USA
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20
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Ongeng D, Geeraerd AH, Springael D, Ryckeboer J, Muyanja C, Mauriello G. Fate ofEscherichia coliO157:H7 andSalmonella entericain the manure-amended soil-plant ecosystem of fresh vegetable crops: A review. Crit Rev Microbiol 2013; 41:273-94. [DOI: 10.3109/1040841x.2013.829415] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Avalos Vizcarra I, Emge P, Miermeister P, Chabria M, Konradi R, Vogel V, Möller J. Fluorescence-based in situ assay to probe the viability and growth kinetics of surface-adhering and suspended recombinant bacteria. Biointerphases 2013; 8:22. [PMID: 24706134 PMCID: PMC4243816 DOI: 10.1186/1559-4106-8-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/16/2013] [Indexed: 01/24/2023] Open
Abstract
Bacterial adhesion and biofilm growth can cause severe biomaterial-related infections and failure of medical implants. To assess the antifouling properties of engineered coatings, advanced approaches are needed for in situ monitoring of bacterial viability and growth kinetics as the bacteria colonize a surface. Here, we present an optimized protocol for optical real-time quantification of bacterial viability. To stain living bacteria, we replaced the commonly used fluorescent dye SYTO(®) 9 with endogenously expressed eGFP, as SYTO(®) 9 inhibited bacterial growth. With the addition of nontoxic concentrations of propidium iodide (PI) to the culture medium, the fraction of live and dead bacteria could be continuously monitored by fluorescence microscopy as demonstrated here using GFP expressing Escherichia coli as model organism. The viability of bacteria was thereby monitored on untreated and bioactive dimethyloctadecyl[3-(trimethoxysilyl)propyl]ammonium chloride (DMOAC)-coated glass substrates over several hours. Pre-adsorption of the antimicrobial surfaces with serum proteins, which mimics typical protein adsorption to biomaterial surfaces upon contact with host body fluids, completely blocked the antimicrobial activity of the DMOAC surfaces as we observed the recovery of bacterial growth. Hence, this optimized eGFP/PI viability assay provides a protocol for unperturbed in situ monitoring of bacterial viability and colonization on engineered biomaterial surfaces with single-bacteria sensitivity under physiologically relevant conditions.
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Affiliation(s)
- Ima Avalos Vizcarra
- Department of Health Sciences and Technology, Laboratory of Applied Mechanobiology, ETH Zurich, CH-8093, Zurich, Switzerland,
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22
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Dai J, Yoon SH, Sim HY, Yang YS, Oh TK, Kim JF, Hong JW. Charting microbial phenotypes in multiplex nanoliter batch bioreactors. Anal Chem 2013; 85:5892-9. [PMID: 23581968 DOI: 10.1021/ac400648z] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
High-throughput growth phenotyping is receiving great attention for establishing the genotype-phenotype map of sequenced organisms owing to the ready availability of complete genome sequences. To date, microbial growth phenotypes have been investigated mostly by the conventional method of batch cultivation using test tubes, Erlenmeyer flasks, or the recently available microwell plates. However, the current batch cultivation methods are time- and labor-intensive and often fail to consider sophisticated environmental changes. The implementation of batch cultures at the nanoliter scale has been difficult because of the quick evaporation of the culture medium inside the reactors. Here, we report a microfluidic system that allows independent cell cultures in evaporation-free multiplex nanoliter reactors under different culture conditions to assess the behavior of cells. The design allows three experimental replicates for each of eight culture environments in a single run. We demonstrate the versatility of the device by performing growth curve experiments with Escherichia coli and microbiological assays of antibiotics against the opportunistic pathogen Pseudomonas aeruginosa. Our study highlights that the microfluidic system can effectively replace the traditional batch culture methods with nanoliter volumes of bacterial cultivations, and it may be therefore promising for high-throughput growth phenotyping as well as for single-cell analyses.
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Affiliation(s)
- Jing Dai
- Materials Research and Education Center, Department of Mechanical Engineering, Auburn University, Auburn, Alabama 36849, USA
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23
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Two programmed cell death systems in Escherichia coli: an apoptotic-like death is inhibited by the mazEF-mediated death pathway. PLoS Biol 2012; 10:e1001281. [PMID: 22412352 PMCID: PMC3295820 DOI: 10.1371/journal.pbio.1001281] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 01/26/2012] [Indexed: 12/17/2022] Open
Abstract
A newly discovered apoptotic-like death is inhibited by the previously described mazEF-mediated death pathway, revealing two programmed cell death systems in Escherichia coli. In eukaryotes, the classical form of programmed cell death (PCD) is apoptosis, which has as its specific characteristics DNA fragmentation and membrane depolarization. In Escherichia coli a different PCD system has been reported. It is mediated by the toxin–antitoxin system module mazEF. The E. coli mazEF module is one of the most thoroughly studied toxin–antitoxin systems. mazF encodes a stable toxin, MazF, and mazE encodes a labile antitoxin, MazE, which prevents the lethal effect of MazF. mazEF-mediated cell death is a population phenomenon requiring the quorum-sensing pentapeptide NNWNN designated Extracellular Death Factor (EDF). mazEF is triggered by several stressful conditions, including severe damage to the DNA. Here, using confocal microscopy and FACS analysis, we show that under conditions of severe DNA damage, the triggered mazEF-mediated cell death pathway leads to the inhibition of a second cell death pathway. The latter is an apoptotic-like death (ALD); ALD is mediated by recA and lexA. The mazEF-mediated pathway reduces recA mRNA levels. Based on these results, we offer a molecular model for the maintenance of an altruistic characteristic in cell populations. In our model, the ALD pathway is inhibited by the altruistic EDF-mazEF-mediated death pathway. The enteric bacterium Escherichia coli, like most other bacteria, carries on its chromosome a pair of genes, mazE and mazF (mazEF): mazF specifies a toxin, and mazE specifies an antitoxin. Previously, we have shown that E. coli mazEF is responsible for bacterial programmed cell death in response to stressors such as DNA damage. Here, we report that extensive DNA damage can induce a second mode of cell death, which we call apoptotic-like death (ALD). ALD is like apoptosis—a mode of cell death that has previously been recorded only in eukaryotes. During ALD, the cell membrane is depolarized, and the DNA is fragmented and can be detected using the classical TUNEL assay. The MazEF death pathway, however, shows neither of those features, yet also kills the cell. We show that ALD is mediated by two proteins, RecA and LexA, which are noteworthy because LexA is an inhibitor of the SOS response (which is a global response to DNA damage in which the cell cycle is arrested and DNA repair is induced). This defines ALD as a form of SOS response. Furthermore, MazEF and its downstream components cause reduction of recA mRNA levels, which could explain how the MazEF pathway inhibits the ALD pathway. We conclude that the E. coli ALD pathway is a back-up system for the traditional mazEF cell death pathway. Should one of the components of the mazEF pathway be inactivated, bacterial cell death would occur through ALD. These findings also have implications for the mechanisms of “altruistic” cell death among bacterial populations.
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Glutamine synthetase and glucose-6-phosphate isomerase are adhesive moonlighting proteins of Lactobacillus crispatus released by epithelial cathelicidin LL-37. J Bacteriol 2012; 194:2509-19. [PMID: 22389474 DOI: 10.1128/jb.06704-11] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glutamine synthetase (GS) and glucose-6-phosphate isomerase (GPI) were identified as novel adhesive moonlighting proteins of Lactobacillus crispatus ST1. Both proteins were bound onto the bacterial surface at acidic pHs, whereas a suspension of the cells to pH 8 caused their release into the buffer, a pattern previously observed with surface-bound enolase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of L. crispatus. The pH shift was associated with a rapid and transient increase in cell wall permeability, as measured by cell staining with propidium iodide. A gradual increase in the release of the four moonlighting proteins was also observed after the treatment of L. crispatus ST1 cells with increasing concentrations of the antimicrobial cationic peptide LL-37, which kills bacteria by disturbing membrane integrity and was here observed to increase the cell wall permeability of L. crispatus ST1. At pH 4, the fusion proteins His(6)-GS, His(6)-GPI, His(6)-enolase, and His(6)-GAPDH showed localized binding to cell division septa and poles of L. crispatus ST1 cells, whereas no binding to Lactobacillus rhamnosus GG was detected. Strain ST1 showed a pH-dependent adherence to the basement membrane preparation Matrigel. Purified His(6)-GS and His(6)-GPI proteins bound to type I collagen, and His(6)-GS also bound to laminin, and their level of binding was higher at pH 5.5 than at pH 6.5. His(6)-GS also expressed a plasminogen receptor function. The results show the strain-dependent surface association of moonlighting proteins in lactobacilli and that these proteins are released from the L. crispatus surface after cell trauma, under conditions of alkaline stress, or in the presence of the antimicrobial peptide LL-37 produced by human cells.
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25
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Simões LC, Lemos M, Pereira AM, Abreu AC, Saavedra MJ, Simões M. Persister cells in a biofilm treated with a biocide. BIOFOULING 2011; 27:403-11. [PMID: 21547756 DOI: 10.1080/08927014.2011.579599] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
This study investigated the physiology and behaviour following treatment with ortho-phthalaldehyde (OPA), of Pseudomonas fluorescens in both the planktonic and sessile states. Steady-state biofilms and planktonic cells were collected from a bioreactor and their extracellular polymeric substances (EPS) were extracted using a method that did not destroy the cells. Cell structure and physiology after EPS extraction were compared in terms of respiratory activity, morphology, cell protein and polysaccharide content, and expression of the outer membrane proteins (OMP). Significant differences were found between the physiological parameters analysed. Planktonic cells were more metabolically active, and contained greater amounts of proteins and polysaccharides than biofilm cells. Moreover, biofilm formation promoted the expression of distinct OMP. Additional experiments were performed with cells after EPS extraction in order to compare the susceptibility of planktonic and biofilm cells to OPA. Cells were completely inactivated after exposure to the biocide (minimum bactericidal concentration, MBC = 0.55 ± 0.20 mM for planktonic cells; MBC = 1.7 ± 0.30 mM for biofilm cells). After treatment, the potential of inactivated cells to recover from antimicrobial exposure was evaluated over time. Planktonic cells remained inactive over 48 h while cells from biofilms recovered 24 h after exposure to OPA, and the number of viable and culturable cells increased over time. The MBC of the recovered biofilm cells after a second exposure to OPA was 0.58 ± 0.40 mM, a concentration similar to the MBC of planktonic cells. This study demonstrates that persister cells may survive in biocide-treated biofilms, even in the absence of EPS.
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Affiliation(s)
- Lúcia C Simões
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Portugal
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26
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Pablos C, van Grieken R, Marugán J, Moreno B. Photocatalytic inactivation of bacteria in a fixed-bed reactor: Mechanistic insights by epifluorescence microscopy. Catal Today 2011. [DOI: 10.1016/j.cattod.2010.10.051] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Ferreira C, Pereira AM, Pereira MC, Melo LF, Simoes M. Physiological changes induced by the quaternary ammonium compound benzyldimethyldodecylammonium chloride on Pseudomonas fluorescens. J Antimicrob Chemother 2011; 66:1036-43. [DOI: 10.1093/jac/dkr028] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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28
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Sjøholm OR, Nybroe O, Aamand J, Sørensen J. 2,6-Dichlorobenzamide (BAM) herbicide mineralisation by Aminobacter sp. MSH1 during starvation depends on a subpopulation of intact cells maintaining vital membrane functions. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2010; 158:3618-3625. [PMID: 20828902 DOI: 10.1016/j.envpol.2010.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 08/04/2010] [Accepted: 08/05/2010] [Indexed: 05/29/2023]
Abstract
Mineralisation capability was studied in the 2,6-dichlorobenzamide (BAM)-degrading Aminobacter sp. MSH1 under growth-arrested conditions. Cells were starved in mineral salts (MS) solution or groundwater before (14)C-labelled BAM (0.1mM) was added. Cell physiology was monitored with a panel of vitality stains combined with flow cytometry to differentiate intact, depolarised and dead cells. Cells starved for up to 3 weeks in MS solution showed immediate growth-linked mineralisation after BAM amendment while a lag-phase was seen after 8 weeks of starvation. In contrast, cells amended with BAM in natural groundwater showed BAM mineralisation but no growth. The cell-specific mineralisation rate was always comparable (10(-16)molCintact cell(-1)day(-1)) independent of media, growth, or starvation period after BAM amendment; lower rates were only observed as BAM concentration decreased. MSH1 seems useful for bioremediation and should be optimised to maintain an intact cell subpopulation as this seems to be the key parameter for successful mineralisation.
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Affiliation(s)
- Ole R Sjøholm
- Department of Agriculture and Ecology, Section of Genetics and Microbiology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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29
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Davis RW, Arango DC, Jones HDT, Van Benthem MH, Haaland DM, Brozik SM, Sinclair MB. Antimicrobial peptide interactions with silica bead supported bilayers and E. coli:
buforin II, magainin II, and arenicin. J Pept Sci 2009; 15:511-22. [DOI: 10.1002/psc.1152] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Carneiro S, Amaral AL, Veloso ACA, Dias T, Peres AM, Ferreira EC, Rocha I. Assessment of physiological conditions inE. colifermentations by epifluorescent microscopy and image analysis. Biotechnol Prog 2009; 25:882-91. [DOI: 10.1002/btpr.134] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Physiology and behavior of Pseudomonas fluorescens single and dual strain biofilms under diverse hydrodynamics stresses. Int J Food Microbiol 2008; 128:309-16. [PMID: 18951643 DOI: 10.1016/j.ijfoodmicro.2008.09.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 08/12/2008] [Accepted: 09/07/2008] [Indexed: 01/18/2023]
Abstract
Three selected Pseudomonas fluorescens strains (the type strain and two strains originally isolated from a dairy processing plant - D3-348 and D3-350) were used to form turbulent and laminar flow-generated biofilms under laboratorial conditions using flow cell reactors with stainless steel substrata. The D3-348 and D3-350 strains were also used to form dual biofilms. Biofilm phenotypic characteristics, such as respiratory activity, total and culturable cells, biomass, total and matrix proteins and polysaccharides were compared. Biofilm mechanical stability, as a major feature involved in biofilm persistence, was also assessed using a rotating device system. The results indicate that hydrodynamic conditions have a remarkable impact on biofilm phenotype. Turbulent biofilms were more active, had more mass per adhesion surface area, a higher number of total and culturable cells, a higher amount of total proteins per gram of biofilm, similar matrix proteins and identical (D3-348 and D3-350 single and dual biofilms) or smaller (type strain) total and matrix polysaccharides content than their laminar counterparts. Biofilms formed by the type strain revealed a considerable higher amount of total and culturable cells and a higher amount of total proteins (turbulent biofilms) and total and matrix polysaccharides per gram of biofilm than single and dual biofilms formed by the other strains. Mechanical stability assays disclosed that biofilms formed by both type and D3-348 strains had the highest resistance to removal when exposed to mechanical stress. Dual strain biofilms population analysis revealed an apparent co-existence, evidencing neutral interactions. The overall results provided useful information regarding a broad spectrum of P. fluorescens biofilm phenotypic parameters, which can contribute to control and model biofilm processes in food industry.
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Vital M, Hammes F, Egli T. Escherichia coli O157 can grow in natural freshwater at low carbon concentrations. Environ Microbiol 2008; 10:2387-96. [PMID: 18507671 DOI: 10.1111/j.1462-2920.2008.01664.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Whereas much information on the die-off of Escherichia coli in the aquatic environment is available, only few data support its growth under such conditions. We therefore investigated batch growth in microcosms containing different types of sterile freshwater. The water samples were inoculated with low starting cell concentrations of E. coli O157 (3 x 10(3) cells ml(-1)) and growth was followed using nucleic acid staining combined with flow cytometry. We demonstrated that E. coli O157 is able to grow in sterile freshwater at low carbon concentrations, which is against the common view that cell numbers decline over time when added to freshwater samples. A correlation between apparent assimilable organic carbon (AOC(app)) concentration and the final cell concentration reached by E. coli O157 was established (P < 0.01). A considerable fraction of the AOC(app) (34 +/- 13%) was used by E. coli O157 but the numerical cell yield was about five-times lower in comparison with the bacterial AOC-test community, which originated from natural freshwater. On average, the maximum specific growth rate (mu(max)) of E. coli O157 growing in sterile freshwater at 30 degrees C was 0.19 +/- 0.07 h(-1). Batch growth assays at five different temperatures revealed a positive influence of temperature on mu(max) of E. coli O157. The results give new information on the behaviour of this common pathogen in the aquatic environment and contribute to microbial risk assessment in order to prevent spreading of water-borne diseases.
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Affiliation(s)
- Marius Vital
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
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Koike S, Krapac IG, Oliver HD, Yannarell AC, Chee-Sanford JC, Aminov RI, Mackie RI. Monitoring and source tracking of tetracycline resistance genes in lagoons and groundwater adjacent to swine production facilities over a 3-year period. Appl Environ Microbiol 2007; 73:4813-23. [PMID: 17545324 PMCID: PMC1951052 DOI: 10.1128/aem.00665-07] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To monitor the dissemination of resistance genes into the environment, we determined the occurrence of tetracycline resistance (Tc(r)) genes in groundwater underlying two swine confinement operations. Monitoring well networks (16 wells at site A and 6 wells at site C) were established around the lagoons at each facility. Groundwater (n = 124) and lagoon (n = 12) samples were collected from the two sites at six sampling times from 2000 through 2003. Total DNA was extracted, and PCR was used to detect seven Tc(r) genes [tet(M), tet(O), tet(Q), tet(W), tet(C), tet(H), and tet(Z)]. The concentration of Tc(r) genes was quantified by real-time quantitative PCR. To confirm the Tc(r) gene source in groundwater, comparative analysis of tet(W) gene sequences was performed on groundwater and lagoon samples. All seven Tc(r) genes were continually detected in groundwater during the 3-year monitoring period at both sites. At site A, elevated detection frequency and concentration of Tc(r) genes were observed in the wells located down-gradient of the lagoon. Comparative analysis of tet(W) sequences revealed that the impacted groundwater contained gene sequences almost identical (99.8% identity) to those in the lagoon, but these genes were not found in background libraries. Novel sequence clusters and unique indigenous resistance gene pools were also found in the groundwater. Thus, antibiotic resistance genes in groundwater are affected by swine manure, but they are also part of the indigenous gene pool.
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Affiliation(s)
- S Koike
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Matsuda K, Tsuji H, Asahara T, Kado Y, Nomoto K. Sensitive quantitative detection of commensal bacteria by rRNA-targeted reverse transcription-PCR. Appl Environ Microbiol 2006; 73:32-9. [PMID: 17071791 PMCID: PMC1797142 DOI: 10.1128/aem.01224-06] [Citation(s) in RCA: 213] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A sensitive rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) method was developed for exact and sensitive enumeration of subdominant bacterial populations. Using group- or species-specific primers for 16S or 23S rRNA, analytical curves were constructed for Escherichia coli, Enterococcus faecalis, Staphylococcus aureus, Clostridium perfringens, and Pseudomonas aeruginosa, and the threshold cycle value was found to be linear up to an RNA amount of 10(-3) cell per RT-PCR. The number of bacteria in culture was determined by RT-qPCR, and the results correlated well with the CFU count over the range from 10(0) to 10(5) CFU. The bacterial counts obtained by RT-qPCR were the same as the CFU counts irrespective of the growth phase in vitro, except for C. perfringens during starvation periods; the viable cell counts obtained by using a combination of 4',6-diamidino-2-phenylindole (DAPI) staining and SYTO9-propidium iodide double staining were in good agreement with the RT-qPCR counts rather than with the CFU counts. The RT-qPCR method could detect endogenous Enterobacteriaceae and P. aeruginosa in feces of hospitalized patients (n = 38) at a level of 10(3) cells per g of feces, and for enumeration of S. aureus or P. aeruginosa spiked into human peripheral blood, the lower detection limit for RT-qPCR quantification of the bacteria was 2 cells per ml of blood, suggesting that this method was equivalent to the conventional culture method. As only 5 h was needed for RT-qPCR quantification, we suggest that rRNA-targeted RT-qPCR assays provide a sensitive and convenient system for quantification of commensal bacteria and for examining their possible invasion of a host.
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Affiliation(s)
- Kazunori Matsuda
- Yakult Central Institute for Microbiological Research, 1796 Yaho, Kunitachi, Tokyo 186-8650, Japan.
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John DE, Rose JB. Review of factors affecting microbial survival in groundwater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2005; 39:7345-56. [PMID: 16245801 DOI: 10.1021/es047995w] [Citation(s) in RCA: 157] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
This review quantitatively examines a number of published studies that evaluated survival and inactivation of public-health-related microorganisms in groundwater. Information from reviewed literature is used to express microbial inactivation in terms of log10 decline per day for comparison to other studies and organisms. The geometric mean value for inactivation rates for coliphage, poliovirus, echovirus, coliform bacteria, enterococci, and Salmonella spp. were similar at approximately 0.07-0.1 log10 day(-1), while geometric mean inactivation rates for hepatitis A virus, coxsackievirus, and phage PRD-1 were somewhat less at 0.02-0.04 log10 day(-1). Viruses show a temperature dependency with greater inactivation at greater temperatures; however this occurs largely at temperatures greater than 20 degrees C. Coliform bacteria die off in groundwater does not show the temperature dependency that viruses show, likely indicating a complex interplay of inactivation and reproduction subject to influences from native groundwater organisms, temperature, and water chemistry. The presence of native microorganisms seems to negatively impact E. coli survival more so than viruses, but in most cases, nonsterile conditions led to a greater inactivation for viruses also. The effect of attachment to solid surfaces appears to be virus-type-dependent, with PRD-1 more rapidly inactivated as a result of attachment and hepatitis A and poliovirus survival prolonged when attached.
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Affiliation(s)
- David E John
- College of Marine Science, University of South Florida, 140 Seventh Ave South, St. Petersburg, Florida 33701, USA.
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Lehtinen J, Nuutila J, Lilius EM. Green fluorescent protein-propidium iodide (GFP-PI) based assay for flow cytometric measurement of bacterial viability. Cytometry A 2005; 60:165-72. [PMID: 15290717 DOI: 10.1002/cyto.a.20026] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Several staining protocols have been developed for flow cytometric analysis of bacterial viability. One promising method is dual staining with the LIVE/DEAD BacLight bacterial viability kit. In this procedure, cells are treated with two different DNA-binding dyes (SYTO9 and PI), and viability is estimated according to the proportion of bound stain. SYTO9 diffuses through the intact cell membrane and binds cellular DNA, while PI binds DNA of damaged cells only. This dual-staining method allows effective separation between viable and dead cells, which is far more difficult to achieve with single staining. Although SYTO9-PI dual staining is practical for various bacterial viability analyses, the method has a number of disadvantages. Specifically, the passage of SYTO9 through the cell membrane is a slow process, which is significantly accelerated when the integrity of the cell membrane is disrupted. As a result, SYTO9 binding to DNA is considerably enhanced. PI competes for binding sites with SYTO9 and may displace the bound dye. These properties diminish the reliability of the LIVE/DEAD viability kit. In this study, we investigate an alternative method for measuring bacterial viability using a combination of green fluorescent protein (GFP) and PI, with a view to improving data reliability. METHODS Recombinant Escherichia coli cells with a plasmid containing the gene for jellyfish GFP were stained with PI, and green and red fluorescence were measured by FCM. For comparison, cells containing the plasmid from which gfp was removed were stained with SYTO9 and PI, and analyzed by FCM. Viability was estimated according to the proportion of green and red fluorescence. In addition, bioluminescence and plate counting (other methods to assess viability) were used as reference procedures. RESULTS SYTO9-PI dual staining of bacterial cells revealed three different cell populations: living, compromised, and dead cells. These cell populations were more distinct when the GFP-PI combination was used instead of dual staining. No differences in sensitivity were observed between the two methods. However, substitution of SYTO9 with GFP accelerated the procedure. Bioluminescence and plate counting results were in agreement with flow cytometric viability data. CONCLUSIONS In bacterial viability analyses, the GFP-PI combination provided better distinction between current viability stages of E. coli cells than SYTO9-PI dual staining. Additionally, the overall procedure was more rapid. No marked differences in sensitivity were observed.
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Affiliation(s)
- Janne Lehtinen
- Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland.
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Simões M, Pereira MO, Vieira MJ. Validation of respirometry as a short-term method to assess the efficacy of biocides. BIOFOULING 2005; 21:9-17. [PMID: 16019387 DOI: 10.1080/08927010500066982] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
This study shows that a short-term respirometric measurement based on the rate of oxygen uptake needed to oxidize glucose is a reliable and fast method to assess biocide efficacy against P. fluorescens cells. Respiratory activity using oxygen consumption rate, the determination of viable and nonviable cells using Live/Dead BacLight kit and colony formation units (CFU), were compared as indicators of the biocidal efficacy of ortho-phthalaldehyde (OPA). The results showed that determining the effect of OPA against P. fluorescens using the different methods leads to different conclusions. The minimum bactericidal concentration (MBC) was 80 mgl(-1), 100 mgl(-1) and 65 mgl(-1) respectively, using respiratory activity, viability using BacLight counts and culturability. The plate count method was shown to underestimate the biocidal action of OPA, whilst data from respirometry and viability using Live/Dead BacLight kit correlated strongly and were not statistically different when yellow cells were considered nonviable. Respirometry therefore represents an expeditious, non-destructive and accurate method to determine the antimicrobial action of biocides against aerobic heterotrophic bacteria.
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Affiliation(s)
- M Simões
- Centro de Engenharia Biológica, Universidade do Minho, Braga, Portugal
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Affiliation(s)
- Reiner Wiest
- Department of Internal Medicine I, University Hospital Regensburg, Germany
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Maraha N, Backman A, Jansson JK. Monitoring physiological status of GFP-tagged Pseudomonas fluorescens SBW25 under different nutrient conditions and in soil by flow cytometry. FEMS Microbiol Ecol 2004; 51:123-32. [PMID: 16329861 DOI: 10.1016/j.femsec.2004.07.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2004] [Revised: 07/12/2004] [Accepted: 07/26/2004] [Indexed: 10/26/2022] Open
Abstract
Pseudomonas fluorescens SBW25, a plant growth promoting bacterium, has been widely studied due to its potential as an inoculum for improving crop yields. Environmental inoculants are usually applied on seeds or directly to soil and to effectively promote plant growth they need to be viable and active. However, it is difficult to study the physiological status of specific microorganisms in complex environments, such as soil. In this study, our aim was to use molecular tools to specifically monitor the physiological status of P. fluorescens SBW25 in soil and in pure cultures incubated under different nutritional conditions. The cells were previously tagged with marker genes (encoding green fluorescent protein and bacterial luciferase) to specifically track the cells in environmental samples. The physiological status of the cells was determined using the viability stains 5-cyano-2,3-ditolyl-tetrazolium chloride (CTC) and propidium iodide (PI), which stain active and dead cells, respectively. Luciferase activity was used to monitor the metabolic activity of the population. Most of the cells died after incubation for nine days in nutrient rich medium. By contrast when incubated under starvation conditions, most of the population was not stained with CTC or PI (i.e. intact but inactive cells), indicating that most of the cells were presumably dormant. In soil, a large fraction of the SBW25 cell population became inactive and died, as determined by a decline in luciferase activity and CTC-stained cells, an increase in PI-stained cells, and an inability of the cells to be cultured on agar medium. However, approximately 60% of the population was unstained, presumably indicating that the cells entered a state of dormancy in soil similar to that observed under starvation conditions in pure cultures. These results demonstrate the applicability of this approach for monitoring the physiological status of specific cells under stress conditions, such as those experienced by environmental inoculants in soil.
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Affiliation(s)
- Ninwe Maraha
- Section for Natural Sciences, Södertörn University College, Huddinge, Sweden
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Backman A, Maraha N, Jansson JK. Impact of temperature on the physiological status of a potential bioremediation inoculant, Arthrobacter chlorophenolicus A6. Appl Environ Microbiol 2004; 70:2952-8. [PMID: 15128556 PMCID: PMC404409 DOI: 10.1128/aem.70.5.2952-2958.2004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Arthrobacter chlorophenolicus A6 (A6) can degrade large amounts of 4-chlorophenol in soil at 5 and 28 degrees C. In this study, we investigated the effects of temperature on the physiological status of this bacterium in pure culture and in soil. A derivative of A6 tagged with the gfp gene (encoding green fluorescent protein [GFP]) was used to specifically quantify A6 cells in soil. In addition, cyano-ditolyl-tetrazoliumchloride was used to stain GFP-fluorescent cells with an active electron transfer system ("viable cells") whereas propidium iodide (PI) was used to stain cells with damaged membranes ("dead cells"). Another derivative of the strain (tagged with the firefly luciferase gene [luc]) was used to monitor the metabolic activity of the cell population, since the bioluminescence phenotype is dependent on cellular energy reserves. When the cells were incubated in soil at 28 degrees C, the majority were stained with PI, indicating that they had lost their cell integrity. In addition, there was a corresponding decline in metabolic activity and in the ability to be grown in cultures on agar plates after incubation in soil at 28 degrees C, indicating that the cells were dying under those conditions. When the cells were incubated in soil at 5 degrees C, by contrast, the majority of the cells remained intact and a large fraction of the population remained metabolically active. A similar trend towards better cell survival at lower temperatures was found in pure-culture experiments. These results make A. chlorophenolicus A6 a good candidate for the treatment of chlorophenol-contaminated soil in cold climates.
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Affiliation(s)
- Agneta Backman
- Section for Natural Sciences, Södertörn University College, Huddinge, Sweden
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Roslev P, Bjergbaek LA, Hesselsoe M. Effect of oxygen on survival of faecal pollution indicators in drinking water. J Appl Microbiol 2004; 96:938-45. [PMID: 15078509 DOI: 10.1111/j.1365-2672.2004.02209.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS The aim of this study was to determine the effect of oxygen on the survival of faecal pollution indicators including Escherichia coli in nondisinfected drinking water. METHODS AND RESULTS Aerobic and anaerobic drinking water microcosms were inoculated with E. coli ATCC 25922 or raw sewage. Survival of E. coli was monitored by membrane filtration combined with cultivation on standard media, and by in situ hybridization with 16S rRNA-targeted fluorescent oligonucleotide probes. Anaerobic conditions significantly increased the survival of E. coli in drinking water compared with aerobic conditions. Escherichia coli ATCC 25922 showed a biphasic decrease in survival under aerobic conditions with an initial first-order decay rate of -0.11 day(-1) followed by a more rapid rate of -0.35 day(-1). In contrast, the first-order decay rate under anaerobic conditions was only -0.02 day(-1). After 35 days, <0.01% of the initial E. coli ATCC 25922 population remained detectable in aerobic microcosms compared with 48% in anaerobic microcosms. A poor survival was observed under aerobic conditions regardless of whether E. coli ATCC 25922 or sewage-derived E. coli was examined, and regardless of the detection method used (CFU or fluorescent in situ hybridization). Aerobic conditions in drinking water also appeared to decrease the survival of faecal enterococci, somatic coliphages and coliforms other than E. coli. CONCLUSIONS The results indicate that oxygen is a major regulator of the survival of E. coli in nondisinfected drinking water. The results also suggest that faecal pollution indicators other than E. coli may persist longer in drinking water under anaerobic conditions. SIGNIFICANCE AND IMPACT OF THE STUDY The effect of oxygen should be considered when evaluating the survival potential of enteric pathogens in oligotrophic environments.
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Affiliation(s)
- P Roslev
- Section of Environmental Engineering, Department of Life Sciences, Aalborg University, Aalborg, Denmark.
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Liao CH, Shollenberger LM. Survivability and long-term preservation of bacteria in water and in phosphate-buffered saline. Lett Appl Microbiol 2003; 37:45-50. [PMID: 12803555 DOI: 10.1046/j.1472-765x.2003.01345.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To evaluate the suitability of using sterile water and phosphate-buffered saline (PBS) for preservation of bacteria pathogenic to plants or humans. METHODS AND RESULTS The stationary-phase bacterial cells collected from rich agar media were transferred to 10 ml of sterile water or PBS (pH 7.2) containing KH2PO4, 15.44 microm; NaCl, 1.55 mm; Na2HPO4, 27.09 microm in a screw-cap tube. The tubes were sealed with parafilm membranes and stored in the dark and at room temperature. Almost all the bacteria tested (148 strains), including Pseudomonas fluorescens, P. viridiflava, Erwinia spp., Xanthomonas campestris, Cytophaga johnsonae, Salmonella spp., Yersinia enterocolitica, Escherichia coli O157:H7, Listeria monocytogenes and Staphylococcus aureus, survived in water for at least several months and up to 16 years. A vast majority of the Gram-negative bacteria tested survived equally well in water and in PBS for at least 30 weeks. However, the populations of two Gram-positive bacteria [G(+)], L. monocytogenes and Staph. aureus, declined more rapidly in water than in PBS. CONCLUSIONS Plant- and human-pathogenic bacteria can be preserved in pure water or PBS for several years. G(+) bacteria appear to survive better in PBS than in water. SIGNIFICANCE AND IMPACT OF THE STUDY The method described here is a simple and economical means for preservation of bacterial cultures, which is especially useful for laboratories not equipped with the lyophilizer or ultra-low freezer. Long-term survival of food-borne pathogens in water underlines the importance of water as a potential vehicle for transmitting the diseases.
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Affiliation(s)
- C-H Liao
- Food Safety Intervention Technologies Research Unit, US Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Wyndmoor, PA 19038, USA.
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Nancharaiah YV, Wattiau P, Wuertz S, Bathe S, Mohan SV, Wilderer PA, Hausner M. Dual labeling of Pseudomonas putida with fluorescent proteins for in situ monitoring of conjugal transfer of the TOL plasmid. Appl Environ Microbiol 2003; 69:4846-52. [PMID: 12902279 PMCID: PMC169129 DOI: 10.1128/aem.69.8.4846-4852.2003] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe here a dual-labeling technique involving the green fluorescent protein (GFP) and the red fluorescent protein (DsRed) for in situ monitoring of horizontal gene transfer via conjugation. A GFPmut3b-tagged derivative of narrow-host-range TOL plasmid (pWWO) was delivered to Pseudomonas putida KT2442, which was chromosomally labeled with dsRed by transposon insertion via biparental mating. Green and red fluorescent proteins were coexpressed in donor P. putida cells. Cells expressing both fluorescent proteins were smaller in size than cells expressing GFP alone. Donors and transconjugants in mixed culture or sludge samples were discriminated on the basis of their fluorescence by using confocal laser scanning microscopy. Conjugal plasmid transfer frequencies on agar surfaces and in sludge microcosms were determined microscopically without cultivation. This method worked well for in situ monitoring of horizontal gene transfer in addition to tracking the fate of microorganisms released into complex environments. To the best of our knowledge, this is the first study that discusses the coexpression of GFP and DsRed for conjugal gene transfer studies.
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Affiliation(s)
- Y Venkata Nancharaiah
- Institute of Water Quality and Waste Management, Technical University of Munich, Garching 85748, Germany
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Abstract
A significant number of pathogenic microorganisms can be found in environmental reservoirs (air, water, soil). It is important to assess the viability status of these organisms to determine whether they pose a threat to public health. Classical methods for determining viability are time consuming. Hence, molecular methods have been developed to address this problem. Molecular methods offer speed, sensitivity and specificity. Both DNA and RNA have been analysed using molecular amplification methods such as polymerase chain reaction (PCR), reverse transcriptase PCR (RT-PCR) and nucleic acid sequence-based amplification (NASBA). However, due to the variable persistence of nucleic acids in cells post-death, the correlation between presence of DNA and RNA and viability is not clear-cut. Similarly, the choice of target and sensitivity of the method can significantly affect the validity of the viability assay. This review assesses the molecular methods currently available and evaluates their ability to assess cell viability with emphasis on environmental pathogens.
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Affiliation(s)
- J T Keer
- BioAnalytical Innovation Team, LGC Limited, Queens Road, Teddington, Middlesex TW11 0LY, UK.
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