1
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Eitzmann DR, Shamsaei D, Anderson JL. Versatile dual-channel loop-mediated isothermal amplification assay featuring smartphone imaging enables determination of fecal indicator bacteria in environmental waters. Talanta 2023; 265:124890. [PMID: 37421790 DOI: 10.1016/j.talanta.2023.124890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/30/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
Rapid diagnostic assays are often a critical tool for monitoring water quality in developing and developed countries. Conventional testing requires 24-48 h for incubation, resulting in delayed remediation and increasing the likelihood of negative outcomes. In this study, we report a workflow for detection of E. coli, a common indicator of fecal contamination. Following large volume filtration, E. coli is then solubilized enabling the facile isolation and recovery of genetic material by a thin film microextraction (TFME) device featuring a polymeric ionic liquid (PIL) sorbent. Rapid recovery of pure nucleic acids is achieved using a PIL sorbent with high affinity for DNA to significantly increase mass transfer and facilitate adsorption and desorption of DNA. Downstream detection is performed by a versatile, dual channel loop mediated isothermal amplification (LAMP) assay featuring a colorimetric dye and a sequence-specific molecular beacon. A portable LAMP companion box enables consistent isothermal heating and endpoint smartphone imaging while being powered by a single 12-V battery. Programmable LEDs are switched from white or blue light to facilitate the independent imaging of the colorimetric dye or fluorometric probe following amplification. The methodology positively identified E. coli in environmental samples spiked to concentrations of 6600 colony forming units (CFU) per milliliter and 660 CFU/mL with 100% and 22% positivity, respectively.
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Affiliation(s)
- Derek R Eitzmann
- Department of Chemistry, Iowa State University, Ames, IA, 50011, United States
| | - Danial Shamsaei
- Department of Chemistry, Iowa State University, Ames, IA, 50011, United States
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA, 50011, United States.
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2
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Ersoy Omeroglu E, Bayer A, Sudagidan M, Ozalp VC, Yasa I. The Effects of Paddy Cultivation and Microbiota Members on Arsenic Accumulation in Rice Grain. Foods 2023; 12:foods12112155. [PMID: 37297400 DOI: 10.3390/foods12112155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
Access to safe food is one of the most important issues. In this context, rice plays a prominent role. Because high levels of arsenic in rice grain are a potential concern for human health, in this study, we determined the amounts of arsenic in water and soil used in the rice development stage, changes in the arsC and mcrA genes using qRT-PCR, and the abundance and diversity (with metabarcoding) of the dominant microbiota. When the rice grain and husk samples were evaluated in terms of arsenic accumulation, the highest values (1.62 ppm) were obtained from areas where groundwater was used as irrigation water, whereas the lowest values (0.21 ppm) occurred in samples from the stream. It was observed that the abundance of the Comamonadaceae family and Limnohabitans genus members was at the highest level in groundwater during grain formation. As rice development progressed, arsenic accumulated in the roots, shoots, and rice grain. Although the highest arsC values were reached in the field where groundwater was used, methane production increased in areas where surface water sources were used. In order to provide arsenic-free rice consumption, the preferred soil, water source, microbiota members, rice type, and anthropogenic inputs for use on agricultural land should be evaluated rigorously.
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Affiliation(s)
- Esra Ersoy Omeroglu
- Basic and Industrial Microbiology Section, Biology Department, Faculty of Science, Ege University, Bornova, 35100 Izmir, Türkiye
| | - Asli Bayer
- Basic and Industrial Microbiology Section, Biology Department, Faculty of Science, Ege University, Bornova, 35100 Izmir, Türkiye
| | - Mert Sudagidan
- Department of Medical Biology, Medical School, Atilim University, 06830 Ankara, Türkiye
| | - Veli Cengiz Ozalp
- Department of Medical Biology, Medical School, Atilim University, 06830 Ankara, Türkiye
| | - Ihsan Yasa
- Basic and Industrial Microbiology Section, Biology Department, Faculty of Science, Ege University, Bornova, 35100 Izmir, Türkiye
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3
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Jamal RB, Vitasovic T, Gosewinkel U, Ferapontova EE. Detection of E.coli 23S rRNA by electrocatalytic "off-on" DNA beacon assay with femtomolar sensitivity. Biosens Bioelectron 2023; 228:115214. [PMID: 36906990 DOI: 10.1016/j.bios.2023.115214] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023]
Abstract
Prevention of food spoilage, environmental bio-contamination, and pathogenic infections requires rapid and sensitive bacterial detection systems. Among microbial communities, the bacterial strain of Escherichia coli is most widespread, with pathogenic and non-pathogenic strains being biomarkers of bacterial contamination. Here, we have developed a fM-sensitive, simple, and robust electrocatalytically-amplified assay facilitating specific detection of E.coli 23S ribosomal rRNA, in the total RNA sample, after its site-specific cleavage by RNase H enzyme. Gold screen-printed electrodes (SPE) were electrochemically pre-treated to be productively modified with a methylene-blue (MB) - labelled hairpin DNA probes, which hybridization with the E. coli-specific DNA placed MB in the top region of the DNA duplex. The formed duplex acted as an electrical wire, mediating electron transfer from the gold electrode to the DNA-intercalated MB, and further to ferricyanide in solution, enabling its electrocatalytic reduction otherwise impeded on the hairpin-modified SPEs. The assay facilitated 20 min 1 fM detection of both synthetic E. coli DNA and 23S rRNA isolated from E.coli (equivalent to 15 CFU mL-1), and can be extended to fM analysis of nucleic acids isolated from any other bacteria.
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Affiliation(s)
- Rimsha B Jamal
- Interdisciplinary Nanoscience Center (iNANO) and Aarhus University Center for Water Technology (WATEC), Faculty of Science, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Toni Vitasovic
- Interdisciplinary Nanoscience Center (iNANO) and Aarhus University Center for Water Technology (WATEC), Faculty of Science, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Ulrich Gosewinkel
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000, Roskilde, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and Aarhus University Center for Water Technology (WATEC), Faculty of Science, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.
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Khan IUH, Murdock A, Mahmud M, Cloutier M, Benoit T, Bashar S, Patidar R, Mi R, Daneshfar B, Farenhorst A, Kumar A. Quantitative Assessment of First Nations Drinking Water Distribution Systems for Detection and Prevalence of Thermophilic Campylobacter Species. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10466. [PMID: 36078183 PMCID: PMC9518054 DOI: 10.3390/ijerph191710466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/03/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Water is considered a major route for transmitting human-associated pathogens. Although microbial water quality indicators are used to test for the presence of waterborne pathogens in drinking water, the two are poorly correlated. The current study investigates the prevalence of thermophilic DNA markers specific for Campylobacter spp. (C. jejuni and C. coli) in source water and throughout the water distribution systems of two First Nations communities in Manitoba, Canada. A total of 220 water samples were collected from various points of the drinking water distribution system (DWDS) between 2016 and 2018. Target Campylobacter spp. were always (100%) detected in a home with a fiberglass (CF) cistern, as well as the community standpipe (SP). The target bacteria were also frequently detected in treated water at the Water Treatment Plant (WTP) (78%), homes with polyethylene (CP) (60%) and concrete (CC) (58%) cisterns, homes with piped (P) water (43%) and water truck (T) samples (20%), with a maximum concentration of 1.9 × 103 cells 100 mL-1 (C. jejuni) and 5.6 × 105 cells 100 mL-1 (C. coli). Similarly, target bacteria were detected in 68% of the source water samples with a maximum concentration of 4.9 × 103 cells 100 mL-1 (C. jejuni) and 8.4 × 105 cells 100 mL-1 (C. coli). Neither target Campylobacter spp. was significantly associated with free and total chlorine concentrations in water. The study results indicate that there is an immediate need to monitor Campylobacter spp. in small communities of Canada and, particularly, to improve the DWDS in First Nations communities to minimize the risk of Campylobacter infection from drinking water sources. Further research is warranted in improving/developing processes and technologies to eliminate microbial contaminants from water.
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Affiliation(s)
- Izhar U. H. Khan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
| | - Anita Murdock
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Maria Mahmud
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
| | - Michel Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
| | - Thomas Benoit
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Sabrin Bashar
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Rakesh Patidar
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ruidong Mi
- Department of Soil Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Bahram Daneshfar
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON K1A 0C6, Canada
| | - Annemieke Farenhorst
- Department of Soil Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Tian T, Dai S, Liu D, Wang Y, Qiao W, Yang M, Zhang Y. Occurrence and transfer characteristics of bla CTX-M genes among Escherichia coli in anaerobic digestion systems treating swine waste. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:155321. [PMID: 35452730 DOI: 10.1016/j.scitotenv.2022.155321] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/12/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
Livestock waste is a known reservoir of Escherichia coli (E. coli) carrying clinically important CTX-M-type extended-spectrum β-lactamase genes (blaCTX-M), however, the occurrence and transfer characteristics of blaCTX-M genes during anaerobic digestion (AD) remain unclear. Herein, four full-scale and two parallel lab-scale AD systems treating swine waste under ambient and mesophilic conditions were investigated by both molecular- and culture-based methods to reveal the occurrence and transfer behaviors of blaCTX-M genes during AD. Real-time TaqMan polymerase chain reaction revealed 1.3 × 104-6.8 × 105 and 3.0 × 104-7.0 × 105 copies/mL of blaCTX-M groups 1 and 9 in all feeding substrates. While AD reduced the absolute abundance of groups 1 and 9 by 0.63-2.24 and 0.08-1.30 log (P < 0.05), 5.0 × 102-4.1 × 103 and 1.1 × 104-3.5 × 104 copies/mL of groups 1 and 9 remained in the anaerobic effluent, respectively. In total, 141 blaCTX-M-carrying E. coli isolates resistant to cefotaxime were obtained from the AD reactors. Whole-genome sequencing showed that blaCTX-M-65 mainly carried by E. coli ST155 was the most frequently detected group 9 subtype in the feeding substrate; whereas blaCTX-M-14 associated with the dominant clones E. coli ST6802 and ST155 became the major subtype in AD effluent. Furthermore, blaCTX-M-14 was flanked by ΔIS26 upstream and ΔIS903B downstream. The ΔIS26-blaCTX-M-14-ΔIS903B element was mainly located on the IncHI2 plasmid in E. coli ST48 and ST6802 and also the IncFIB plasmid in ST155 in anaerobic effluent. Conjugation assays showed that the plasmids harboring blaCTX-M-14 could be successfully transferred at a frequency of 10-3-10-2 cells per recipient cell. This study revealed that blaCTX-M genes remained in both the full-scale and lab-scale AD effluents of swine waste. Thus, additional efforts should be implemented to block the discharge and spread of antibiotic resistance genes to the environment.
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Affiliation(s)
- Tiantian Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiting Dai
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dejun Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Wei Qiao
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Occurrence of Antibiotic Resistant Bacteria in Urban Karst Groundwater Systems. WATER 2022. [DOI: 10.3390/w14060960] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Antibiotic resistance is a global concern for human, animal, and environmental health. Many studies have identified wastewater treatment plants and surface waters as major reservoirs of antibiotic resistant bacteria (ARB) and genes (ARGs). Yet their prevalence in urban karst groundwater systems remains largely unexplored. Considering the extent of karst groundwater use globally, and the growing urban areas in these regions, there is an urgent need to understand antibiotic resistance in karst systems to protect source water and human health. This study evaluated the prevalence of ARGs associated with resistance phenotypes at 10 urban karst features in Bowling Green, Kentucky weekly for 46 weeks. To expand the understanding of prevalence in urban karst, a spot sampling of 45 sites in the Tampa Bay Metropolitan area, Florida was also conducted. Specifically, this study considered tetracycline and extended spectrum beta-lactamase (ESBLs) producing, including third generation cephalosporin, resistant E. coli, and tetracycline and macrolide resistant Enterococcus spp. across the 443 Kentucky and 45 Florida samples. A consistent prevalence of clinically relevant and urban associated ARGs were found throughout the urban karst systems, regardless of varying urban development, karst geology, climate, or landuse. These findings indicate urban karst groundwater as a reservoir for antibiotic resistance, potentially threatening human health.
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7
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Antibiotic resistance and phylogenetic profiling of Escherichia coli from dairy farm soils; organic versus conventional systems. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100088. [PMID: 34977826 PMCID: PMC8688864 DOI: 10.1016/j.crmicr.2021.100088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/20/2021] [Accepted: 11/29/2021] [Indexed: 12/25/2022] Open
Abstract
First known comparison of antimicrobial resistance traits in E. coli strains from new zealand farms practicing organic and conventional husbandry. Potential extended spectrum β-lactamase producing strains isolated from dairy farm environments. Organic dairy farms tended to harbour fewer resistant isolates than those recovered from conventionally farmed counterparts. Evidence for anthroponotic transmission of resistant strains of human origin to farm environments. Implications for the spread of antimicrobial resistance traits from farm environments discussed.
The prevalence and spread of antimicrobial resistance (AMR) as a result of the persistent use and/or abuse of antimicrobials is a key health problem for health authorities and governments worldwide. A study of contrasting farming systems such as organic versus conventional dairy farming may help to authenticate some factors that may contribute to the prevalence and spread of AMR in their soils. A case study was conducted in organic and conventional dairy farms in the South Canterbury region of New Zealand. A total of 814 dairy farm soil E. coli (DfSEC) isolates recovered over two years were studied. Isolates were recovered from each of two farms practicing organic, and another two practicing conventional husbandries. The E. coli isolates were examined for their antimicrobial resistance (AMR) against cefoxitin, cefpodoxime, chloramphenicol, ciprofloxacin, gentamicin, meropenem, nalidixic acid, and tetracycline. Phylogenetic relationships were assessed using an established multiplex PCR method. The AMR results indicated 3.7% of the DfSEC isolates were resistant to at least one of the eight selected antimicrobials. Of the resistant isolates, DfSEC from the organic dairy farms showed a lower prevalence of resistance to the antimicrobials tested, compared to their counterparts from the conventional farms. Phylogenetic analysis placed the majority (73.7%) of isolates recovered in group B1, itself dominated by isolates of bovine origin. The tendency for higher rates of resistance among strains from conventional farming may be important for future decision-making around farming practices Current husbandry practices may contribute to the prevalence and spread of AMR in the industry.
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Saeed MA, Syed EH, Ghafor A, Yaqub T, Javeed A, Waheed U. Evaluation of Analytical Sensitivity of Sdf I based PCR and Sandwich ELISA for Salmonella Enteritidis detection and On-Farm prevalence in Punjab, Pakistan. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2022. [DOI: 10.1590/1806-9061-2021-1492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- MA Saeed
- University of Veterinary and Animal Sciences, Pakistan
| | - EH Syed
- University of Veterinary and Animal Sciences, Pakistan
| | - A Ghafor
- University of Veterinary and Animal Sciences, Pakistan
| | - T Yaqub
- University of Veterinary and Animal Sciences, Pakistan
| | - A Javeed
- University of Veterinary and Animal Sciences, Pakistan
| | - U Waheed
- University of Veterinary and Animal Sciences, Pakistan
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A Model System for Sensitive Detection of Viable E. coli Bacteria Combining Direct Viability PCR and a Novel Microarray-Based Detection Approach. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9120357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We established an innovative approach that included direct, viability, and nested PCR for rapid and reliable identification of the fecal indicator organism Escherichia coli (E. coli). Direct PCR enabled successful amplification of the target uidA gene, omitting a prior DNA isolation or purification step. Furthermore, we applied viability PCR (v-PCR) to ensure the detection of only relevant viable bacterial cells. The principle involves the binding of propidium monoazide (PMA), a selective nucleic acid intercalating dye, to accessible DNA of heat killed bacteria cells and, consequently, allows viable and heat killed E. coli cells to be discriminated. To ensure high sensitivity, direct v-PCR was followed by a nested PCR step. The resulting amplicons were analyzed by a rapid 30 min microarray-based DNA hybridization assay for species-specific DNA detection of E. coli. A positive signal was indicated by enzymatically generated silver nanoparticle deposits, which served as robust endpoint signals allowing an immediate visual readout. The presented novel protocol allows the detection of 1 × 101 viable E. coli cells per PCR run.
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Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis. WATER 2021. [DOI: 10.3390/w13243551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
With increasing concerns about public health and the development of molecular techniques, new detection tools and the combination of existing approaches have increased the abilities of pathogenic bacteria monitoring by exploring new biomarkers, increasing the sensitivity and accuracy of detection, quantification, and analyzing various genes such as functional genes and antimicrobial resistance genes (ARG). Molecular methods are gradually emerging as the most popular detection approach for pathogens, in addition to the conventional culture-based plate enumeration methods. The analysis of pathogens in wastewater and the back-estimation of infections in the community, also known as wastewater-based epidemiology (WBE), is an emerging methodology and has a great potential to supplement current surveillance systems for the monitoring of infectious diseases and the early warning of outbreaks. However, as a complex matrix, wastewater largely challenges the analytical performance of molecular methods. This review synthesized the literature of typical pathogenic bacteria in wastewater, types of biomarkers, molecular methods for bacterial analysis, and their recent advances in wastewater analysis. The advantages and limitation of these molecular methods were evaluated, and their prospects in WBE were discussed to provide insight for future development.
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Tian T, Qiao W, Han Z, Wen X, Yang M, Zhang Y. Effect of temperature on the persistence of fecal bacteria in ambient anaerobic digestion systems treating swine manure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 791:148302. [PMID: 34126495 DOI: 10.1016/j.scitotenv.2021.148302] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/19/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
This study aimed to explore the effect of temperature on the persistence of fecal bacteria by multiple approaches in ambient anaerobic digestion systems treating swine manure. Both lab-scale (15 °C, 20 °C, and 25 °C) and field (26 °C on average) studies were conducted by high-throughput sequencing and culture-based methods. A community-wide Bayesian SourceTracker method was used to identify and estimate the fecal bacterial proportion in anaerobic effluent. High proportional contributions of fecal bacteria were observed in effluent at 15 °C (73%) and 20 °C (75%), while less was found at 25 °C (19%). This was further verified by a field study (23%) and an anaerobic reactor study at 37 °C (0.01%). To explore the potential reasons for differences in fecal bacterial proportions, bacterial taxa were divided into "lost" and "survivor" taxa in manure waste by LEfSe. The "survivor" taxa abundance was positively correlated with SourceTracker proportion (r = 0.913, P = 0.001), but negatively correlated with temperature (r = -0.826, P = 0.006). In addition, biomarkers in effluent were divided into "enriched" and "de novo" taxa. "Enriched" taxa, including acidogenic and acetogenic bacteria, were found at all temperatures, whereas taxa related to organic degradation were multiplied "de novo" at 25 °C. Variation partition analysis showed that temperature could explain 30% of variations in effluent bacterial community. Moreover, coliforms isolated from the manure and effluents at 15 °C and 20 °C were also phylogenetically related. This study provided comprehensive insight into the impact of temperature on the persistence of fecal bacteria in anaerobic effluent, with temperatures over 25 °C recommended to reduce fecal pollution.
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Affiliation(s)
- Tiantian Tian
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Qiao
- College of Engineering, China Agricultural University, Beijing 100083, China
| | - Ziming Han
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianghua Wen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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12
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Chen A, Wang D, Nugen SR, Chen J. An Engineered Reporter Phage for the Fluorometric Detection of Escherichia coli in Ground Beef. Microorganisms 2021; 9:microorganisms9020436. [PMID: 33669833 PMCID: PMC7922204 DOI: 10.3390/microorganisms9020436] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/11/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022] Open
Abstract
Despite enhanced sanitation implementations, foodborne bacterial pathogens still remain a major threat to public health and generate high costs for the food industry. Reporter bacteriophage (phage) systems have been regarded as a powerful technology for diagnostic assays for their extraordinary specificity to target cells and cost-effectiveness. Our study introduced an enzyme-based fluorescent assay for detecting the presence of E. coli using the T7 phage engineered with the lacZ operon which encodes beta-galactosidase (β-gal). Both endogenous and overexpressed β-gal expression was monitored using a fluorescent-based method with 4-methylumbelliferyl β-d-galactopyranoside (MUG) as the substrate. The infection of E. coli with engineered phages resulted in a detection limit of 10 CFU/mL in ground beef juice after 7 h of incubation. In this study, we demonstrated that the overexpression of β-gal coupled with a fluorogenic substrate can provide a straightforward and sensitive approach to detect the potential biological contamination in food samples. The results also suggested that this system can be applied to detect E. coli strains isolated from environmental samples, indicating a broader range of bacterial detection.
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Affiliation(s)
- Anqi Chen
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; (A.C.); (D.W.); (J.C.)
| | - Danhui Wang
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; (A.C.); (D.W.); (J.C.)
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA
| | - Sam R. Nugen
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; (A.C.); (D.W.); (J.C.)
- Correspondence:
| | - Juhong Chen
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA; (A.C.); (D.W.); (J.C.)
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, USA
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Abdelrasoul GN, Anwar A, MacKay S, Tamura M, Shah MA, Khasa DP, Montgomery RR, Ko AI, Chen J. DNA aptamer-based non-faradaic impedance biosensor for detecting E. coli. Anal Chim Acta 2020; 1107:135-144. [PMID: 32200887 DOI: 10.1016/j.aca.2020.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/31/2020] [Accepted: 02/02/2020] [Indexed: 02/07/2023]
Abstract
Developing a real-time, portable, and inexpensive sensor for pathogenic bacteria is crucial since the conventional detection approaches such as enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) assays are high cost, time-consuming, and require an expert operator. Here we present a portable, inexpensive, and convenient impedance-based biosensor using Interdigitated Electrode (IDE) arrays to detect Escherichia coli (E. coli) as a model to demonstrate the feasibility of an impedance-based biosensor. We manipulated the affinity of the IDE array towards E. coli (E. coli BL21 series) by functionalizing the IDEs' surface with an E. coli outer membrane protein (OMP) Ag1 Aptamer. To determine the dominant factors affecting the sensitivity and the performance of the biosensor in detecting E. coli, we investigated the roles of the substrate material used in the fabrication of the IDE, the concentration of the aptamer, and the composition of the carboxy aliphatic thiol mixture used in the pre-treatment of the IDE surface. In the sensing experiments we used an E. coli concentration range of 25-1000 cfu mL-1 and confirmed the binding of the OMP Ag1 Aptamer to the outer membrane protein of the E. coli by Field Emission Scanning Electron Microscopy (FESEM), Optical Microscopy, and Atomic Force Microscopy (AFM). By tuning the surface chemistry, the IDEs' substrate material, and the concentration of the OMP Ag1 Aptamer, our sensor could detect E. coli with the analytical sensitivity of approximately 1.8 Ohm/cfu and limit of detection of 9 cfu mL-1. We found that the molecular composition of the self-assembled monolayer (SAM) formed on the top of the IDEs before the attachment of the OMP Ag1 Aptamer significantly impacted the sensitivity of the sensor. Notably, with straightforward changes to the molecular recognition elements, this platform device can be used to detect a wide range of other microorganisms and chemicals relevant for environmental monitoring and public health.
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Affiliation(s)
- Gaser N Abdelrasoul
- Electrical, and Computer Engineering Department, University of Alberta, Edmonton, AB, Canada
| | - Afreen Anwar
- Electrical, and Computer Engineering Department, University of Alberta, Edmonton, AB, Canada; Department of Botany, University of Kashmir, Srinagar, 190006, J&K, India
| | - Scott MacKay
- Electrical, and Computer Engineering Department, University of Alberta, Edmonton, AB, Canada
| | - Marcus Tamura
- Electrical, and Computer Engineering Department, University of Alberta, Edmonton, AB, Canada
| | - Manzoor A Shah
- Department of Botany, University of Kashmir, Srinagar, 190006, J&K, India
| | - Damase P Khasa
- Centre for Forest Research (CEF), Institute for Integrative and Systems Biology (IBIS), and Canada Research Chair in Forest and Environmental Genomics, Université Laval, Québec, QC, G1V0A6, Canada
| | - Ruth R Montgomery
- Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Jie Chen
- Electrical, and Computer Engineering Department, University of Alberta, Edmonton, AB, Canada.
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14
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Imran M, Ehrhardt CJ, Bertino MF, Shah MR, Yadavalli VK. Chitosan Stabilized Silver Nanoparticles for the Electrochemical Detection of Lipopolysaccharide: A Facile Biosensing Approach for Gram-Negative Bacteria. MICROMACHINES 2020; 11:mi11040413. [PMID: 32295278 PMCID: PMC7231338 DOI: 10.3390/mi11040413] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/06/2020] [Accepted: 04/12/2020] [Indexed: 11/25/2022]
Abstract
Negatively charged lipopolysaccharide (LPS), a major endotoxin and component of the outer membrane of several Gram-negative bacteria, provides a useful biomarker for the indirect detection of these pathogens. For instance, Escherichia coli (E. coli) is a pathogenic bacterium that causes infections in almost all age groups, and has been implicated in food and water contamination. Current diagnostic and detection methods tend to be labor-intensive or expensive, necessitating the need for an easy, sensitive, rapid, and low-cost method. We report on the synthesis and use of positively charged chitosan stabilized silver nanoparticles (Chi-AgNPs) as a sensitive electrochemical nanobiosensor for the detection of LPS. Chi-AgNPs were synthesized through a facile, single step protocol, and characterized for size, charge, and morphology. Glassy carbon electrodes modified with Chi-AgNPs resulted in an enhancement of signal in the presence of both LPS and E. coli. Detection was accomplished over a large concentration range (several orders of magnitude) of 0.001–100 ng/mL and 10–107 CFU/mL. The biosensors can reliably detect LPS and E. coli at very low concentrations. Chi-AgNPs have potential as low cost, sensitive nanobiosensors for Gram-negative bacteria due to strong electrostatic interaction with LPS present in their outer membranes.
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Affiliation(s)
- Muhammad Imran
- Department of Chemical & Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA;
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi 75270, Pakistan;
| | | | - Massimo F. Bertino
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Muhammad R. Shah
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi 75270, Pakistan;
| | - Vamsi K. Yadavalli
- Department of Chemical & Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284, USA;
- Correspondence: ; Tel.: +1-804-828-0587
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15
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Nie W, Wang J, Xu J, Yao L, Qiao D, Xue F, Tang F, Chen W. A molecule capturer analysis system for visual determination of avian pathogenic Escherichia coli serotype O78 using a lateral flow assay. Mikrochim Acta 2020; 187:198. [PMID: 32130536 DOI: 10.1007/s00604-020-4170-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 02/18/2020] [Indexed: 01/11/2023]
Abstract
A method for rapid and accurate determination of avian pathogenic Escherichia coli serotype O78 (APEC O78) by the gold nanoparticle-labeled lateral flow strip method, entitled molecule capturer analysis system (MCAS), is described. Target virulence-associated gene of APEC O78 is adopted as the analyte. After pre-amplification with the designed functional primer set, numerous new-formed amplicons are simultaneously labeled with fluorescein isothiocyanate (FITC) and digoxin. AuNPs with a diameter of 18 nm and the characteristic plasmonic peak at 526 nm are utilized for labeling. These two labels of FITC and digoxin are further captured and measured with the AuNP-labeled lateral flow strip, and the AuNPs are retained on the test line through the immunoreaction for signal output. Under optimized conditions, this MCAS protocol can determine the target APEC O78 with excellent determination limit of 4.3 cfu mL-1 based on the optical density of AuNPs on the test line of lateral flow strips. The working range is 2.52 × 101 to 1.63 × 107 cfu mL-1. Spiked serum samples are rapid and accurately measured, and the results are highly correlated with those of the real-time PCR. With this MCAS protocol, rapid and on-site determination of APEC O78 can be realized without expensive instruments or professional personnel. This MCAS protocol can be easily applied to other analytes by just replacing the traditional primer set with functionalization primer set. Graphical abstract Schematic illustration of molecule capturer analysis system for rapid and accurate determination of avian pathogenic Escherichia coli serotype O78.
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Affiliation(s)
- Wenfang Nie
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
- School of Food Science & Biological Engineering, Engineering Research Center of Bio-process, MOE, Hefei University of Technology, Hefei, 230009, China
| | - Juanfang Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianguo Xu
- School of Food Science & Biological Engineering, Engineering Research Center of Bio-process, MOE, Hefei University of Technology, Hefei, 230009, China
| | - Li Yao
- School of Food Science & Biological Engineering, Engineering Research Center of Bio-process, MOE, Hefei University of Technology, Hefei, 230009, China
| | - Dongqing Qiao
- School of Food Science & Biological Engineering, Engineering Research Center of Bio-process, MOE, Hefei University of Technology, Hefei, 230009, China
| | - Feng Xue
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fang Tang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Wei Chen
- School of Food Science & Biological Engineering, Engineering Research Center of Bio-process, MOE, Hefei University of Technology, Hefei, 230009, China.
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16
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Zhang X, Wang X, Yang Q, Jiang X, Li Y, Zhao J, Qu K. Conductometric sensor for viable Escherichia coli and Staphylococcus aureus based on magnetic analyte separation via aptamer. Mikrochim Acta 2019; 187:43. [PMID: 31832780 DOI: 10.1007/s00604-019-3880-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 09/29/2019] [Indexed: 11/28/2022]
Abstract
A method is described to determine viable populations of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus). The method employs aptamer-magnetic separation combined with resistivity based detection. The bacteria were separated by means of aptamer-functionalized magnetic beads. They were then quantified by measuring their growth kinetics through time-dependent conductivity changes of culture media. The time-course of growth was logged by real-time and contactless measurements that yielded starting concentrations from the duration of lag intervals prior to the log phase of growth. In pure water samples, the linear ranges for measuring E. coli and S. aureus cells are 2.5 × 103-2.5 × 108 CFU·mL-1 and 4.1 × 103-4.1 × 108 CFU·mL-1, respectively. In spiked tap water samples, the lower limits of detection are 2.3 × 104 CFU·mL-1 and 4.0 × 103 CFU·mL-1 for E. coli and S. aureus, with recoveries of 87.0-108.7% and 92.5-105.0%, respectively. The relative standard deviation of these measurements (10.0%) is below that of plate counting method (13.9%). The presence of micro/nanoparticles such as magnetic beads or selenium nanoparticles in the culture media does not interfere, unlike in case of automatted optical density monitoring. The E. coli and S. aureus cells captured on the aptamer-functionalized magnetic beads can be directly tested for their susceptibility to antibiotics. The process of magnetic separation and determination of load burden requires neither bulky, sophisticated equipment nor expensive reagents. Graphical abstractAptamer-functionalized magnetic beads are used to selectively capture and separate E. coli and S. aureus cells in aqueous samples. They are directly transferred to a multichannel conductometric sensor for the quantification of viable bacteria via automated monitoring of their growth kinetics.
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Affiliation(s)
- Xuzhi Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, China
| | - Xiaochun Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Qianqian Yang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiaoyu Jiang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,College of Marine Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Yang Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Jun Zhao
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Keming Qu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266071, China.
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Deshmukh R, Bhand S, Roy U. A novel method for rapid and sensitive detection of viable Escherichia coli cells using UV-induced PMA-coupled quantitative PCR. Braz J Microbiol 2019; 51:773-778. [PMID: 31654340 DOI: 10.1007/s42770-019-00161-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 09/17/2019] [Indexed: 02/07/2023] Open
Abstract
We report a specific and sensitive method to improve the coupling of propidium monoazide (PMA) with DNA derived from killed cells of Escherichia coli using UV light of 365 nm. UV light of three different intensities mainly 2.4 × 103, 4.8 × 103, and 7.2 × 103 μJ/cm2 was applied to E. coli cells each for 1, 3, and 5 min. PMA was found to be successfully cross-linked with the DNA from killed cells of E. coli at 4.8 × 103 μJ/cm2 in 3 min leading to the complete inhibition of PCR amplification of DNA derived from PMA-treated heat-killed cells. In spiked phosphate-buffered saline and potable water samples, the difference of the Cq values between PMA-treated viable cells and PMA-untreated viable cells ranged from -0.17 to 0.2, demonstrating that UV-induced PMA activation had a negligible effect on viable cells. In contrast, the difference of the Cq values between PMA-treated heat-killed cells and PMA-untreated heat-killed cells ranged from 8.9 to 9.99, indicating the ability of PMA to inhibit PCR amplification of DNA derived from killed cells to an equivalent as low as 100 CFU. In conclusion, this UV-coupled PMA-qPCR assay provided a rapid and sensitive methodology to selectively detect viable E. coli cells in spiked water samples within 4 h.
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Affiliation(s)
- Rehan Deshmukh
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Goa Campus, NH17B Bypass, Goa, 403726, India
| | - Sunil Bhand
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Goa Campus, NH17B Bypass, Goa, 403726, India
| | - Utpal Roy
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, Goa Campus, NH17B Bypass, Goa, 403726, India.
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18
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Luk AW, Beckmann S, Manefield M. Dependency of DNA extraction efficiency on cell concentration confounds molecular quantification of microorganisms in groundwater. FEMS Microbiol Ecol 2019; 94:5066166. [PMID: 30137345 DOI: 10.1093/femsec/fiy146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 08/01/2018] [Indexed: 12/13/2022] Open
Abstract
Quantification of microbes in water systems is essential to industrial practices ranging from drinking water and wastewater treatment to groundwater remediation. While quantification using DNA-based molecular methods is precise, the accuracy is dependent on DNA extraction efficiencies. We show that the DNA yield is strongly impacted by the cell concentration in groundwater samples (r = -0.92, P < 0.0001). This has major implications for industrial applications using quantitative polymerase chain reaction (qPCR) to determine cell concentrations in water, including bioremediation. We propose a simple normalization method using a DNA recovery ratio, calculated with the total cell count and DNA yield. Application of this method to enumeration of bacteria and archaea in groundwater samples targeting phylogenetic markers (16S rRNA) demonstrated an increased goodness of fit after normalization (7.04 vs 0.94 difference in Akaike's information criteria). Furthermore, normalization was applied to qPCR quantification of functional genes and combined with DNA sequencing of archaeal and bacterial 16S rRNA genes to monitor changes in abundance of methanogenic archaea and sulphate-reducing bacteria in groundwater. The integration of qPCR and DNA sequencing with appropriate normalization enables high-throughput quantification of microbial groups using increasingly affordable and accessible techniques. This research has implications for microbial ecology and engineering research as well as industrial practice.
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Affiliation(s)
- Alison Ws Luk
- School of Chemical Engineering, University of New South Wales, NSW 2052, Australia
| | - Sabrina Beckmann
- School of Chemical Engineering, University of New South Wales, NSW 2052, Australia
| | - Mike Manefield
- School of Chemical Engineering, University of New South Wales, NSW 2052, Australia.,School of Civil and Environmental Engineering, University of New South Wales, NSW 2052, Australia
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19
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Yuan Y, Zheng G, Lin M, Mustapha A. Detection of viable Escherichia coli in environmental water using combined propidium monoazide staining and quantitative PCR. WATER RESEARCH 2018; 145:398-407. [PMID: 30173100 DOI: 10.1016/j.watres.2018.08.044] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 07/31/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
The objectives of this study were to specifically detect viable Escherichia coli in environmental waters by targeting the ycjM gene in a propidium monoazide (PMA)-qPCR assay. PMA is a viability dye that can inhibit the amplification of DNA from dead cells, thus allowing for the detection and quantification of only viable cells. The ycjM primers were used to target E. coli that directly originated from the feces of warm blooded animals, and avoid false positive detection caused by "naturalized" E. coli that can exist in the environment. In this study, tap water and environmental waters were inoculated with E. coli isolated from animal feces. Following cell collection, samples were treated with PMA, followed by DNA isolation and qPCR detection. For pure cultures, 5 μM PMA with a 10-min light exposure was efficient at inhibiting the amplification of DNA from 105 CFU/mL dead E. coli cells, with a detection limit of 102 CFU/100 mL viable cells. For tap and environmental waters collected in the winter, a 10 μM PMA was required and as low as 103 CFU/100 mL viable cells could be detected in the presence of 105 CFU/100 mL dead cells. For water samples collected during the summer, 102 CFU/10 mL viable cells could be detected in the presence of 104 CFU/10 mL dead cells, after a 20 μM PMA treatment. No significant differences were found among the PMA-qPCR assay and two other standard culture-based methods for detection of viable E. coli in environmental water. In conclusion, with proper pretreatment of environmental water samples, this PMA-qPCR assay that targets the ycjM gene could quantify viable E. coli cells that directly come from the feces of warm-blooded animals, and therefore effectively and accurately indicate the quality of environmental water.
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Affiliation(s)
- Yuan Yuan
- Food Science Program, Division of Food Systems and Bioengineering, 246 Stringer Wing, Eckles Hall, University of Missouri, Columbia, MO, 65211, USA
| | - Guolu Zheng
- Department of Agriculture and Environmental Sciences, Lincoln University of Missouri, USA
| | - Mengshi Lin
- Food Science Program, Division of Food Systems and Bioengineering, 246 Stringer Wing, Eckles Hall, University of Missouri, Columbia, MO, 65211, USA
| | - Azlin Mustapha
- Food Science Program, Division of Food Systems and Bioengineering, 246 Stringer Wing, Eckles Hall, University of Missouri, Columbia, MO, 65211, USA.
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20
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Wealleans AL, Walsh MC, Romero LF, Ravindran V. Comparative effects of two multi-enzyme combinations and a Bacillus probiotic on growth performance, digestibility of energy and nutrients, disappearance of non-starch polysaccharides, and gut microflora in broiler chickens. Poult Sci 2018; 96:4287-4297. [PMID: 29053809 PMCID: PMC5850647 DOI: 10.3382/ps/pex226] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/04/2017] [Indexed: 12/01/2022] Open
Abstract
The efficacy of two exogenous enzyme combinations and a multi-strain Bacillus probiotic (DFM) on the growth performance, nutrient digestibility, disappearance of non-starch polysaccharides (NSP) and gut microbial composition was investigated in broilers. One-day old Ross 308 chicks were assigned to 36 pens with 22 birds/pen and 6 pens/treatment (Experiment 1) or 36 cages with 8 birds/cage and 6 cages/treatment (Experiment 2). Treatment additives were added to nutritionally complete corn/soy based starter (d 1 to 21) and finisher (d 22 to 42) diets. Treatments included 1) a control diet containing 500 FTU/kg phytase (CTL), 2) CTL + xylanase (2,000 U/kg) and amylase (200 U/kg; XA), 3) CTL+XA + protease (4000 U/g; XAP), 4) CTL+DFM (150,000 cfu/g of 3 strains of Bacillus spp), 5) CTL+DFM+XA, and 6) CTL+DFM+XAP. Supplementation with DFM increased BW, BWG, and FI compared with the CTL (P < 0.05); XAP, but not XA, resulted in increased final BW, BWG and FI compared to the control (P < 0.05). XA and XAP improved apparent ileal digestibility (AID) of starch and fat on d 22 to 42 with XAP improving AMEn (by ∼82 kcal) compared with CTL birds (P < 0.01). DFM+XAP improved apparent ileal digestible energy (AIDE), AID of fat and starch on d 22 to 42, and additionally had a greater than additive effect on AIDE and AMEn. Supplementation with DFM+XAP reduced the ileal and total tract flow of insoluble arabinose and additionally total tract flow of soluble and insoluble xylose and total galactose (P < 0.05); similar effects of XA+DFM were not seen or were lower in magnitude, suggesting that the protease component plays an important role in increasing the availability of NSP for hydrolysis. Supplementation with DFM alone did not affect gut bacterial populations, but XA and XAP reduced numbers of Campylobacter species (by > 2.5 log cfu/g; P < 0.001) and Bacteroides (P < 0.02) in the cecum compared with CTL birds.
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Affiliation(s)
- A L Wealleans
- Danisco Animal Nutrition, DuPont Industrial Biosciences, Marlborough, UK
| | - M C Walsh
- Danisco Animal Nutrition, DuPont Industrial Biosciences, Marlborough, UK
| | - L F Romero
- Danisco Animal Nutrition, DuPont Industrial Biosciences, Marlborough, UK
| | - V Ravindran
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North 4442, New Zealand
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21
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Asakura H, Kawase J, Ikeda T, Honda M, Sasaki Y, Uema M, Kabeya H, Sugiyama H, Igimi S, Takai S. Microbiological Quality Assessment of Game Meats at Retail in Japan. J Food Prot 2017; 80:2119-2126. [PMID: 29166176 DOI: 10.4315/0362-028x.jfp-17-137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this study, we examined the prevalence of Shiga toxin-producing Escherichia coli and Salmonella spp. and the distribution of indicator bacteria in 248 samples of game meats (120 venison and 128 wild boar) retailed between November 2015 and March 2016 in Japan. No Salmonella spp. were detected in any of the samples, whereas Shiga toxin-producing Escherichia coli serotype OUT:H25 (stx2d+, eae-) was isolated from one deer meat sample, suggesting a possible source for human infection. Plate count assays indicated greater prevalence of coliforms and E. coli in wild boar meat than in venison, whereas their prevalence in processing facilities showed greater variation than in animal species. The 16S rRNA ion semiconductor sequencing analysis of 24 representative samples revealed that the abundances of Acinetobacter and Arthrobacter spp. significantly correlated with the prevalence of E. coli, and quantitative PCR analyses in combination with selective plate count assay verified these correlations. To our knowledge, this is the first report to characterize the diversity of microorganisms of game meats at retail in Japan, together with identification of dominant microbiota. Our data suggest the necessity of bottom-up hygienic assessment in areas of slaughtering and processing facilities to improve microbiological safety.
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Affiliation(s)
- Hiroshi Asakura
- 1 Division of Biomedical Food Research, National Institute of Health Sciences, Kamiyoga 1-18-1, Setagaya-ku, Tokyo 158-8501, Japan
| | - Jun Kawase
- 2 Shimane Prefectural Meat Inspection Centre, Asayama-cho senzan 1677-2, Ota, Shimane 699-2212, Japan
| | - Tetsuya Ikeda
- 3 Department of Infectious Diseases, Hokkaido Institute of Public Health, Kita19 Nishi 12, Kita-ku Sapporo, Hokkaido 060-0819, Japan
| | - Mioko Honda
- 4 Department of Animal Nursing Science, Yamazaki Gakuen University, Minami-Osawa 4-7-2, Hachioji 192-0364, Japan
| | - Yoshimasa Sasaki
- 1 Division of Biomedical Food Research, National Institute of Health Sciences, Kamiyoga 1-18-1, Setagaya-ku, Tokyo 158-8501, Japan
| | - Masashi Uema
- 1 Division of Biomedical Food Research, National Institute of Health Sciences, Kamiyoga 1-18-1, Setagaya-ku, Tokyo 158-8501, Japan
| | - Hidenori Kabeya
- 5 Department of Veterinary Public Health, Nihon University, Kameino 1866, Fujisawa, Kanagawa 252-0880, Japan
| | - Hiromu Sugiyama
- 6 Department of Parasitology, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Shizunobu Igimi
- 7 Department of Microbiology, Tokyo University of Agriculture, Sakuragaoka 1-1, Setagaya-ku, Tokyo 156-8502, Japan; and
| | - Shinji Takai
- 8 Department of Animal Hygiene, Kitasato University, Higashi 23-35-1, Towada, Aomori 034-8628, Japan
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Spoelstra J, Senger ND, Schiff SL. Artificial Sweeteners Reveal Septic System Effluent in Rural Groundwater. JOURNAL OF ENVIRONMENTAL QUALITY 2017; 46:1434-1443. [PMID: 29293857 DOI: 10.2134/jeq2017.06.0233] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
It has been widely documented that municipal wastewater treatment plant effluents are a major source of artificial sweeteners to surface waters. However, in rural areas, the extent to which septic systems contribute these same compounds to groundwater aquifers is largely unknown. We examined the occurrence of four commonly used artificial sweeteners in an unconfined sand aquifer that serves as a water supply for rural residents, as a receptor of domestic wastewater from septic systems, and as a source of baseflow to the Nottawasaga River, ON, Canada. Groundwater from the Lake Algonquin Sand Aquifer in the southern Nottawasaga River Watershed was collected from private domestic wells and as groundwater seeps discharging along the banks of the Nottawasaga River. Approximately 30% of samples had detectable levels of one or more artificial sweeteners, indicating the presence of water derived from septic system effluent. Using acesulfame concentrations to estimate the fraction of septic effluent in groundwater samples, ∼3.4 to 13.6% of the domestic wells had 1% or more of their well water being derived from septic system effluent. Similarly, 2.0 to 4.7% of the groundwater seeps had a septic effluent contribution of 1% or more. No relationship was found between the concentration of acesulfame and the concentration of nitrate, ammonium, or soluble reactive phosphorus in the groundwater, indicating that septic effluent is not the dominant source of nutrients in the aquifer. It is expected that the occurrence of artificial sweeteners in shallow groundwater is widespread throughout rural areas in Canada.
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23
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Gonzales-Gustavson E, Cárdenas-Youngs Y, Calvo M, da Silva MFM, Hundesa A, Amorós I, Moreno Y, Moreno-Mesonero L, Rosell R, Ganges L, Araujo R, Girones R. Characterization of the efficiency and uncertainty of skimmed milk flocculation for the simultaneous concentration and quantification of water-borne viruses, bacteria and protozoa. J Microbiol Methods 2017; 134:46-53. [PMID: 28093213 DOI: 10.1016/j.mimet.2017.01.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/05/2017] [Accepted: 01/08/2017] [Indexed: 10/20/2022]
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Cabal A, Vicente J, Alvarez J, Barasona JA, Boadella M, Dominguez L, Gortazar C. Human influence and biotic homogenization drive the distribution of Escherichia coli virulence genes in natural habitats. Microbiologyopen 2017; 6. [PMID: 28213899 PMCID: PMC5458461 DOI: 10.1002/mbo3.445] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/13/2016] [Accepted: 12/21/2016] [Indexed: 11/08/2022] Open
Abstract
Cattle are the main reservoirs for Shiga-toxin-producing Escherichia coli (STEC), the only known zoonotic intestinal E. coli pathotype. However, there are other intestinal pathotypes that can cause disease in humans, whose presence has been seldom investigated. Thus, our aim was to identify the effects of anthropic pressure and of wild and domestic ungulate abundance on the distribution and diversity of the main human E. coli pathotypes and nine of their representative virulence genes (VGs). We used a quantitative real-time PCR (qPCR) for the direct detection and quantification of the genus-specific gene uidA, nine E. coli VGs (stx1, sxt2, eae, ehxA, aggR, est, elt, bfpA, invA), as well as four genes related to O157:H7 (rfbO157 , fliCH7 ) and O104:H4 (wzxO104 , fliCH4 ) serotypes in animals (feces from deer, cattle, and wild boar) and water samples collected in three areas of Doñana National Park (DNP), Spain. Eight of the nine VGs were detected, being invA, eae, and stx2 followed by stx1, aggR, and ehxA the most abundant ones. In quantitative terms (gene copies per mg of sample), stx1 and stx2 gave the highest values. Significant differences were seen regarding VGs in the three animal species in the three sampled areas. The serotype-related genes were found in all but one sample types. In general, VGs were more diverse and abundant in the northern part of the Park, where the surface waters are more contaminated by human waste and farms. In the current study, we demonstrated that human influence is more relevant than host species in shaping the E. coli VGs spatial pattern and diversity in DNP. In addition, wildlife could be potential reservoirs for other pathotypes different from STEC, however further isolation steps would be needed to completely characterize those E. coli.
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Affiliation(s)
- Adriana Cabal
- VISAVET Health Surveillance Centre, Universidad Complutense, Madrid, Spain.,SaBio IREC, National Wildlife Research Institute (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Joaquin Vicente
- SaBio IREC, National Wildlife Research Institute (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Julio Alvarez
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Jose Angel Barasona
- SaBio IREC, National Wildlife Research Institute (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Mariana Boadella
- SaBio IREC, National Wildlife Research Institute (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Lucas Dominguez
- VISAVET Health Surveillance Centre, Universidad Complutense, Madrid, Spain
| | - Christian Gortazar
- SaBio IREC, National Wildlife Research Institute (CSIC-UCLM-JCCM), Ciudad Real, Spain
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Wang D, Chen J, Nugen SR. Electrochemical Detection of Escherichia coli from Aqueous Samples Using Engineered Phages. Anal Chem 2017; 89:1650-1657. [DOI: 10.1021/acs.analchem.6b03752] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Danhui Wang
- Department
of Food Science, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department
of Food Science, Cornell University, Ithaca, New York 14853, United States
| | - Juhong Chen
- Department
of Food Science, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department
of Food Science, Cornell University, Ithaca, New York 14853, United States
| | - Sam R. Nugen
- Department
of Food Science, University of Massachusetts, Amherst, Massachusetts 01003, United States
- Department
of Food Science, Cornell University, Ithaca, New York 14853, United States
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Osińska A, Korzeniewska E, Harnisz M, Niestępski S. The prevalence and characterization of antibiotic-resistant and virulent Escherichia coli strains in the municipal wastewater system and their environmental fate. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 577:367-375. [PMID: 27816226 DOI: 10.1016/j.scitotenv.2016.10.203] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 06/06/2023]
Abstract
Antibiotics are widely used in human and veterinary medicine and in animal production, which increases their concentrations in aquatic ecosystems and contributes to selective pressure on environmental microorganisms. The objective of this study was to identify antibiotic resistance determinants in Escherichia coli strains isolated from untreated and treated wastewater (UWW and TWW) and from river water sampled downstream and upstream (URW and DRW) from the effluent discharge point. The analyzed antibiotic groups were beta-lactams, tetracyclines and fluoroquinolones which are widely used in human and veterinary medicine. The virulence of the isolated E. coli strains was also analyzed, and their clonal relatedness was determined by ERIC (enterobacterial repetitive intergenic consensus sequence) PCR. The highest counts of bacteria resistant to beta-lactams, tetracyclines and fluoroquinolones were noted in UWW at 6.4×104, 4.2×104 and 3.1×103CFU/mL, respectively. A total of 317 E. coli isolates resistant to at least one group of antibiotics were selected among bacterial isolates from river water and wastewater samples. Nearly 38% of those isolates were resistant to all of the tested antibiotics. The highest percent (43%) of multidrug-resistant isolates was noted in UWW samples. Isolates resistant to beta-lactams most frequently harbored blaTEM and blaOXA genes. The group of genes encoding resistance to tetracyclines was most frequently represented by tetA, tetB and tetK, whereas the qnrS gene was noted in isolates resistant to fluoroquinolones. Virulence genes bfpA (65%), ST (56%) and eae (39%) were most widely distributed in all isolates, regardless of their origin. The results of this experiment reveal the dangers associated with environmental contamination by drug-resistant and virulent E. coli strains distributed with treated wastewater. Multidrug resistance was determined more frequently in strains isolated from DRW than in isolates from URW samples. Our findings provide valuable inputs for evaluating public health hazards associated with bacterial contamination.
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Affiliation(s)
- Adriana Osińska
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland.
| | - Ewa Korzeniewska
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland.
| | - Monika Harnisz
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland.
| | - Sebastian Niestępski
- Department of Environmental Microbiology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Prawocheńskiego 1 Str., 10-720 Olsztyn, Poland.
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Newman MA, Zebeli Q, Velde K, Grüll D, Molnar T, Kandler W, Metzler-Zebeli BU. Enzymatically Modified Starch Favorably Modulated Intestinal Transit Time and Hindgut Fermentation in Growing Pigs. PLoS One 2016; 11:e0167784. [PMID: 27936165 PMCID: PMC5147999 DOI: 10.1371/journal.pone.0167784] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/21/2016] [Indexed: 01/10/2023] Open
Abstract
Aside from being used as stabilizing agents in many processed foods, chemically modified starches may act as functional dietary ingredients. Therefore, development of chemically modified starches that are less digestible in the upper intestinal segments and promote fermentation in the hindgut receives considerable attention. This study aimed to investigate the impact of an enzymatically modified starch (EMS) on nutrient flow, passage rate, and bacterial activity at ileal and post-ileal level. Eight ileal-cannulated growing pigs were fed 2 diets containing 72% purified starch (EMS or waxy cornstarch as control) in a cross-over design for 10 d, followed by a 4-d collection of feces and 2-d collection of ileal digesta. On d 17, solid and liquid phase markers were added to the diet to determine ileal digesta flow for 8 h after feeding. Reduced small intestinal digestion after the consumption of the EMS diet was indicated by a 10%-increase in ileal flow and fecal excretion of dry matter and energy compared to the control diet (P<0.05). Moreover, EMS feeding reduced ileal transit time of both liquid and solid fractions compared to the control diet (P<0.05). The greater substrate flow to the large intestine with the EMS diet increased the concentrations of total and individual short-chain fatty acids (SCFA) in feces (P<0.05). Total bacterial 16S rRNA gene abundance was not affected by diet, whereas the relative abundance of the Lactobacillus group decreased (P<0.01) by 50% and of Enterobacteriaceae tended (P<0.1) to increase by 20% in ileal digesta with the EMS diet compared to the control diet. In conclusion, EMS appears to resemble a slowly digestible starch by reducing intestinal transit and increasing SCFA in the distal large intestine.
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Affiliation(s)
- M. A. Newman
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
- Research Cluster “Animal Gut Health”, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Q. Zebeli
- Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna, Vienna, Austria
- Research Cluster “Animal Gut Health”, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - K. Velde
- Equine University Clinic, Department for Companion Animals and Horses, University of Veterinary Medicine, Vienna, Austria
| | - D. Grüll
- Agrana Research & Innovation Center GmbH, Tulln, Austria
| | - T. Molnar
- Agrana Research & Innovation Center GmbH, Tulln, Austria
| | - W. Kandler
- Center for Analytical Chemistry, Department of Agrobiotechnology, IFA-Tulln, University of Natural Resources and Life Sciences, Vienna, Austria
| | - B. U. Metzler-Zebeli
- Research Cluster “Animal Gut Health”, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria
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Singh G, Vajpayee P, Rani N, Amoah ID, Stenström TA, Shanker R. Exploring the potential reservoirs of non specific TEM beta lactamase (bla(TEM)) gene in the Indo-Gangetic region: A risk assessment approach to predict health hazards. JOURNAL OF HAZARDOUS MATERIALS 2016; 314:121-128. [PMID: 27111425 DOI: 10.1016/j.jhazmat.2016.04.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 03/21/2016] [Accepted: 04/13/2016] [Indexed: 06/05/2023]
Abstract
The emergence of antimicrobial resistant bacteria is an important public health and environmental contamination issue. Antimicrobials of β-lactam group accounts for approximately two thirds, by weight, of all antimicrobials administered to humans due to high clinical efficacy and low toxicity. This study explores β-lactam resistance determinant gene (blaTEM) as emerging contaminant in Indo-Gangetic region using qPCR in molecular beacon format. Quantitative Microbial Risk Assessment (QMRA) approach was adopted to predict risk to human health associated with consumption/exposure of surface water, potable water and street foods contaminated with bacteria having blaTEM gene. It was observed that surface water and sediments of the river Ganga and Gomti showed high numbers of blaTEM gene copies and varied significantly (p<0.05) among the sampling locations. The potable water collected from drinking water facility and clinical settings exhibit significant number of blaTEM gene copies (13±0.44-10200±316 gene copies/100mL). It was observed that E.crassipes among aquatic flora encountered in both the rivers had high load of blaTEM gene copies. The information on prevalence of environmental reservoirs of blaTEM gene containing bacteria in Indo-Gangetic region and risk associated will be useful for formulating strategies to protect public from menace of clinical risks linked with antimicrobial resistant bacteria.
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Affiliation(s)
- Gulshan Singh
- Environmental Microbiology, CSIR - Indian Institute of Toxicology Research, Post Box - 80, Mahatma Gandhi Marg, Lucknow, U.P., India; SARChI Chair, Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Poornima Vajpayee
- Environmental Microbiology, CSIR - Indian Institute of Toxicology Research, Post Box - 80, Mahatma Gandhi Marg, Lucknow, U.P., India
| | - Neetika Rani
- Environmental Microbiology, CSIR - Indian Institute of Toxicology Research, Post Box - 80, Mahatma Gandhi Marg, Lucknow, U.P., India
| | - Isaac Dennis Amoah
- SARChI Chair, Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Thor Axel Stenström
- SARChI Chair, Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Rishi Shanker
- Environmental Microbiology, CSIR - Indian Institute of Toxicology Research, Post Box - 80, Mahatma Gandhi Marg, Lucknow, U.P., India; Institute of Life Sciences, School of Science and Technology, Ahmedabad University, Ahmedabad-380009, Gujarat, India.
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29
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Uyaguari-Diaz MI, Chan M, Chaban BL, Croxen MA, Finke JF, Hill JE, Peabody MA, Van Rossum T, Suttle CA, Brinkman FSL, Isaac-Renton J, Prystajecky NA, Tang P. A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples. MICROBIOME 2016; 4:20. [PMID: 27391119 PMCID: PMC5011856 DOI: 10.1186/s40168-016-0166-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/04/2016] [Indexed: 05/16/2023]
Abstract
BACKGROUND Studies of environmental microbiota typically target only specific groups of microorganisms, with most focusing on bacteria through taxonomic classification of 16S rRNA gene sequences. For a more holistic understanding of a microbiome, a strategy to characterize the viral, bacterial, and eukaryotic components is necessary. RESULTS We developed a method for metagenomic and amplicon-based analysis of freshwater samples involving the concentration and size-based separation of eukaryotic, bacterial, and viral fractions. Next-generation sequencing and culture-independent approaches were used to describe and quantify microbial communities in watersheds with different land use in British Columbia. Deep amplicon sequencing was used to investigate the distribution of certain viruses (g23 and RdRp), bacteria (16S rRNA and cpn60), and eukaryotes (18S rRNA and ITS). Metagenomic sequencing was used to further characterize the gene content of the bacterial and viral fractions at both taxonomic and functional levels. CONCLUSION This study provides a systematic approach to separate and characterize eukaryotic-, bacterial-, and viral-sized particles. Methodologies described in this research have been applied in temporal and spatial studies to study the impact of land use on watershed microbiomes in British Columbia.
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Affiliation(s)
- Miguel I. Uyaguari-Diaz
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Michael Chan
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Bonnie L. Chaban
- South Kensington Campus, Imperial College London, Sir Ernst Chain Building, London, SW7 2AZ UK
| | - Matthew A. Croxen
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
| | - Jan F. Finke
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4 Canada
| | - Michael A. Peabody
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Thea Van Rossum
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8 Canada
| | - Fiona S. L. Brinkman
- Department of Molecular Biology and Biochemistry, South Science Building, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Judith Isaac-Renton
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Natalie A. Prystajecky
- British Columbia Public Health Laboratory, British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4 Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, PO Box 26999, Doha, Qatar
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Deshmukh RA, Joshi K, Bhand S, Roy U. Recent developments in detection and enumeration of waterborne bacteria: a retrospective minireview. Microbiologyopen 2016; 5:901-922. [PMID: 27397728 PMCID: PMC5221461 DOI: 10.1002/mbo3.383] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 04/20/2016] [Accepted: 05/02/2016] [Indexed: 12/17/2022] Open
Abstract
Waterborne diseases have emerged as global health problems and their rapid and sensitive detection in environmental water samples is of great importance. Bacterial identification and enumeration in water samples is significant as it helps to maintain safe drinking water for public consumption. Culture‐based methods are laborious, time‐consuming, and yield false‐positive results, whereas viable but nonculturable (VBNCs) microorganisms cannot be recovered. Hence, numerous methods have been developed for rapid detection and quantification of waterborne pathogenic bacteria in water. These rapid methods can be classified into nucleic acid‐based, immunology‐based, and biosensor‐based detection methods. This review summarizes the principle and current state of rapid methods for the monitoring and detection of waterborne bacterial pathogens. Rapid methods outlined are polymerase chain reaction (PCR), digital droplet PCR, real‐time PCR, multiplex PCR, DNA microarray, Next‐generation sequencing (pyrosequencing, Illumina technology and genomics), and fluorescence in situ hybridization that are categorized as nucleic acid‐based methods. Enzyme‐linked immunosorbent assay (ELISA) and immunofluorescence are classified into immunology‐based methods. Optical, electrochemical, and mass‐based biosensors are grouped into biosensor‐based methods. Overall, these methods are sensitive, specific, time‐effective, and important in prevention and diagnosis of waterborne bacterial diseases.
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Affiliation(s)
- Rehan A Deshmukh
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| | - Kopal Joshi
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| | - Sunil Bhand
- Biosensor Lab, Department of Chemistry, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
| | - Utpal Roy
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani-K.K. Birla Goa Campus, NH17B Bypass, Zuarinagar, Goa, 403726, India
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Książczyk M, Kuczkowski M, Dudek B, Korzekwa K, Tobiasz A, Korzeniowska-Kowal A, Paluch E, Wieliczko A, Bugla-Płoskońska G. Application of Routine Diagnostic Procedure, VITEK 2 Compact, MALDI-TOF MS, and PCR Assays in Identification Procedure of Bacterial Strain with Ambiguous Phenotype. Curr Microbiol 2016; 72:570-82. [PMID: 26804795 DOI: 10.1007/s00284-016-0993-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/19/2015] [Indexed: 11/28/2022]
Abstract
In diagnostic microbiology as well as in microbiological research, the identification of a microorganism is a crucial and decisive stage. A broad choice of methods is available, based on both phenotypic and molecular properties of microbes. The aim of this study was to compare the application of phenotypic and molecular tools in bacterial identification on the example of Gram-negative intestine rod with an ambiguous phenotype. Different methods of identification procedure, which based on various properties of bacteria, were applied, e.g., microscopic observation of single-bacterial cells, macroscopic observation of bacterial colonies morphology, the automated system of microorganism identification (biochemical tests), the mass spectrometry method (analysis of bacterial proteome), and genetic analysis with PCR reactions. The obtained results revealed discrepancies in the identification of the tested bacterial strain with an atypical phenotype: mucous morphology of colonies, not characteristic for either E. coli and Citrobacter spp., mass spectrometry analysis of proteome initially assigned the tested strain to Citrobacter genus (C. freundii) and biochemical profiles pointed to Escherichia coli. A decisive method in the current study was genetic analysis with PCR reactions which identified conserved genetic sequences highly specific to E. coli species in the genome of the tested strain.
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Affiliation(s)
- Marta Książczyk
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63/77, 51-148, Wrocław, Poland.
| | - Maciej Kuczkowski
- Department of Epizootiology and Clinic of Bird and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Pl. Grunwaldzki 45, 50-366, Wrocław, Poland
| | - Bartłomiej Dudek
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63/77, 51-148, Wrocław, Poland
| | - Kamila Korzekwa
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63/77, 51-148, Wrocław, Poland
| | - Anna Tobiasz
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114, Wrocław, Poland
| | - Agnieszka Korzeniowska-Kowal
- Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114, Wrocław, Poland
| | - Emil Paluch
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63/77, 51-148, Wrocław, Poland.,Department Physicochemistry of Microorganisms, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63/77, 51-148, Wrocław, Poland
| | - Alina Wieliczko
- Department of Epizootiology and Clinic of Bird and Exotic Animals, Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences, Pl. Grunwaldzki 45, 50-366, Wrocław, Poland
| | - Gabriela Bugla-Płoskońska
- Department of Microbiology, Institute of Genetics and Microbiology, University of Wrocław, Przybyszewskiego 63/77, 51-148, Wrocław, Poland
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Asakura H, Tachibana M, Taguchi M, Hiroi T, Kurazono H, Makino SI, Kasuga F, Igimi S. Seasonal and Growth-Dependent Dynamics of Bacterial Community in Radish Sprouts. J Food Saf 2016. [DOI: 10.1111/jfs.12256] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Hiroshi Asakura
- Division of Biomedical Food Research; National Institute of Health Sciences; Kamiyoga 1-18-1 Setagaya-ku Tokyo Japan
| | - Masato Tachibana
- Division of Biomedical Food Research; National Institute of Health Sciences; Kamiyoga 1-18-1 Setagaya-ku Tokyo Japan
| | - Masumi Taguchi
- Department of Bacteriology; Osaka Prefectural Institute of Public Health; Nakamichi 1-3-69 Higashinari-ku, Osaka Osaka Japan
| | - Toyoko Hiroi
- Department of Animal and Food Hygiene; Obihiro University of Agriculture and Veterinary Medicine; Nishi 2-11 Inada-cho Obihiro Hokkaido Japan
| | - Hisao Kurazono
- Department of Animal and Food Hygiene; Obihiro University of Agriculture and Veterinary Medicine; Nishi 2-11 Inada-cho Obihiro Hokkaido Japan
| | - Sou-Ichi Makino
- Department of Domestic Science; Kyoto Seibo College; Fukakusa taya-cho, Fushimi-ku, Kyoto Kyoto Japan
| | - Fumiko Kasuga
- Division of Safety Information on Food; Drugs, and Chemicals, National Institute of Health Sciences; Kamiyoga 1-18-1 Setagaya-ku Tokyo Japan
| | - Shizunobu Igimi
- Division of Biomedical Food Research; National Institute of Health Sciences; Kamiyoga 1-18-1 Setagaya-ku Tokyo Japan
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Removal of Fecal Indicators, Pathogenic Bacteria, Adenovirus, Cryptosporidium and Giardia (oo)cysts in Waste Stabilization Ponds in Northern and Eastern Australia. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13010096. [PMID: 26729150 PMCID: PMC4730487 DOI: 10.3390/ijerph13010096] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/23/2015] [Accepted: 12/28/2015] [Indexed: 11/25/2022]
Abstract
Maturation ponds are used in rural and regional areas in Australia to remove the microbial loads of sewage wastewater, however, they have not been studied intensively until present. Using a combination of culture-based methods and quantitative real-time PCR, we assessed microbial removal rates in maturation ponds at four waste stabilization ponds (WSP) with (n = 1) and without (n = 3) baffles in rural and remote communities in Australia. Concentrations of total coliforms, E. coli, enterococci, Campylobacter spp., Salmonella spp., F+ RNA coliphage, adenovirus, Cryptosporidium spp. and Giardia (oo) cysts in maturation ponds were measured at the inlet and outlet. Only the baffled pond demonstrated a significant removal of most of the pathogens tested and therefore was subjected to further study by analyzing E. coli and enterococci concentrations at six points along the baffles over five sampling rounds. Using culture-based methods, we found a decrease in the number of E. coli and enterococci from the initial values of 100,000 CFU per 100 mL in the inlet samples to approximately 1000 CFU per 100 mL in the outlet samples for both bacterial groups. Giardia cysts removal was relatively higher than fecal indicators reduction possibly due to sedimentation.
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Mendes Silva D, Domingues L. On the track for an efficient detection of Escherichia coli in water: A review on PCR-based methods. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 113:400-11. [PMID: 25540852 DOI: 10.1016/j.ecoenv.2014.12.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 12/03/2014] [Accepted: 12/08/2014] [Indexed: 05/11/2023]
Abstract
Ensuring water safety is an ongoing challenge to public health providers. Assessing the presence of fecal contamination indicators in water is essential to protect public health from diseases caused by waterborne pathogens. For this purpose, the bacteria Escherichia coli has been used as the most reliable indicator of fecal contamination in water. The methods currently in use for monitoring the microbiological safety of water are based on culturing the microorganisms. However, these methods are not the desirable solution to prevent outbreaks as they provide the results with a considerable delay, lacking on specificity and sensitivity. Moreover, viable but non-culturable microorganisms, which may be present as a result of environmental stress or water treatment processes, are not detected by culture-based methods and, thus, may result in false-negative assessments of E. coli in water samples. These limitations may place public health at significant risk, leading to substantial monetary losses in health care and, additionally, in costs related with a reduced productivity in the area affected by the outbreak, and in costs supported by the water quality control departments involved. Molecular methods, particularly polymerase chain reaction-based methods, have been studied as an alternative technology to overcome the current limitations, as they offer the possibility to reduce the assay time, to improve the detection sensitivity and specificity, and to identify multiple targets and pathogens, including new or emerging strains. The variety of techniques and applications available for PCR-based methods has increased considerably and the costs involved have been substantially reduced, which together have contributed to the potential standardization of these techniques. However, they still require further refinement in order to be standardized and applied to the variety of environmental waters and their specific characteristics. The PCR-based methods under development for monitoring the presence of E. coli in water are here discussed. Special emphasis is given to methodologies that avoid pre-enrichment during the water sample preparation process so that the assay time is reduced and the required legislated sensitivity is achieved. The advantages and limitations of these methods are also reviewed, contributing to a more comprehensive overview toward a more conscious research in identifying E. coli in water.
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Affiliation(s)
- Diana Mendes Silva
- CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
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Derda R, Lockett MR, Tang SKY, Fuller RC, Maxwell EJ, Breiten B, Cuddemi CA, Ozdogan A, Whitesides GM. Filter-Based Assay for Escherichia coli in Aqueous Samples Using Bacteriophage-Based Amplification. Anal Chem 2013; 85:7213-20. [DOI: 10.1021/ac400961b] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ratmir Derda
- Department of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
- Wyss Institute of Biologically
Inspired Engineering, Harvard University, 60 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department of Chemistry and Alberta
Glycomics Centre, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB T6G 2G2, Canada
| | - Matthew R. Lockett
- Department of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Sindy K. Y. Tang
- Department of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
- Wyss Institute of Biologically
Inspired Engineering, Harvard University, 60 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Renee C. Fuller
- Department of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
| | - E. Jane Maxwell
- Department of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Benjamin Breiten
- Department of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Christine A. Cuddemi
- Department of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Aysegul Ozdogan
- Department of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
| | - George M. Whitesides
- Department of Chemistry and
Chemical Biology, Harvard University, 12
Oxford Street, Cambridge, Massachusetts 02138, United States
- Wyss Institute of Biologically
Inspired Engineering, Harvard University, 60 Oxford Street, Cambridge, Massachusetts 02138, United States
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36
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Ferretti JA, Tran HV, Peterson SJ, Loftin V. Rapid method demonstration project at four New Jersey marine beaches using real time quantitative Polymerase Chain Reaction (qPCR). MARINE POLLUTION BULLETIN 2013; 71:51-63. [PMID: 23623653 DOI: 10.1016/j.marpolbul.2013.03.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/22/2013] [Accepted: 03/28/2013] [Indexed: 05/15/2023]
Abstract
Real time quantitative Polymerase Chain Reaction (qPCR) was used at four marine bathing beaches in New Jersey as part of a demonstration project to evaluate the potential for use of qPCR as part of a routine beach monitoring program. Split sample analyses for Enterococcus spp. using membrane filtration (MF) and qPCR were performed for 11weeks during the summer of 2011 using swimming advisories based on qPCR results. Comparison of qPCR and MF results from split samples indicated that there was an 82% overall agreement rate between the two methods. Results from the qPCR tests were available by noon the same day of sample collection and swimming advisories were posted on a dedicated website. The qPCR method can be more labor intensive and requires a higher level of training to perform, however, qPCR was able to assess beach water quality in a timelier manner compared to conventional MF techniques.
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Affiliation(s)
- James A Ferretti
- Division of Environmental Science and Assessment, USEPA Region 2, 2890 Woodbridge Ave., Edison, NJ 08837, USA.
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37
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Nakayama T, Oishi K. Influence of coffee (Coffea arabica) and galacto-oligosaccharide consumption on intestinal microbiota and the host responses. FEMS Microbiol Lett 2013; 343:161-8. [PMID: 23551139 DOI: 10.1111/1574-6968.12142] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 03/24/2013] [Accepted: 03/25/2013] [Indexed: 12/14/2022] Open
Abstract
Although studies have reported numerous effects of coffee on human health, few studies have examined its specific effects on gut microbiota. This study aimed to clarify the influence of coffee and galacto-oligosaccharide (GOS) consumption on gut microbiota and host responses. After mice consumed coffee and GOS, their intestines were sampled, and the bacterial counts were measured with quantitative RT-PCR. Results showed that GOS consumption significantly increased total bacteria counts in the proximal colon. Although Escherichia coli and Clostridium spp. counts significantly decreased in the proximal colon, Bifidobacterium spp. counts increased remarkably in the same area. A bacterial growth inhibition assay was also conducted, and the results showed that E. coli growth was inhibited only by a coffee agar. Host responses were also investigated, revealing that coffee and GOS consumption remarkably increased aquaporin8 expression in the proximal colon. In conclusion, coffee has antibiotic effects, and GOS significantly decreased E. coli and Clostridium spp. counts, but increased Bifidobacterium spp. counts remarkably. Aquaporin8 expression was also increased with a mixture of coffee and GOS consumption. This is the first study to demonstrate that coffee consumption can regulate gut microbiota and increase aquaporin8, both of which are necessary for maintaining intestinal balance.
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Affiliation(s)
- Tatsuya Nakayama
- International Research Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
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38
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Botes M, de Kwaadsteniet M, Cloete TE. Application of quantitative PCR for the detection of microorganisms in water. Anal Bioanal Chem 2013; 405:91-108. [PMID: 23001336 PMCID: PMC7079929 DOI: 10.1007/s00216-012-6399-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 08/28/2012] [Accepted: 08/29/2012] [Indexed: 11/13/2022]
Abstract
The occurrence of microorganisms in water due to contamination is a health risk and control thereof is a necessity. Conventional detection methods may be misleading and do not provide rapid results allowing for immediate action. The quantitative polymerase chain reaction (qPCR) method has proven to be an effective tool to detect and quantify microorganisms in water within a few hours. Quantitative PCR assays have recently been developed for the detection of specific adeno- and polyomaviruses, bacteria and protozoa in different water sources. The technique is highly sensitive and able to detect low numbers of microorganisms. Quantitative PCR can be applied for microbial source tracking in water sources, to determine the efficiency of water and wastewater treatment plants and act as a tool for risk assessment. Different qPCR assays exist depending on whether an internal control is used or whether measurements are taken at the end of the PCR reaction (end-point qPCR) or in the exponential phase (real-time qPCR). Fluorescent probes are used in the PCR reaction to hybridise within the target sequence to generate a signal and, together with specialised systems, quantify the amount of PCR product. Quantitative reverse transcription polymerase chain reaction (q-RT-PCR) is a more sensitive technique that detects low copy number RNA and can be applied to detect, e.g. enteric viruses and viable microorganisms in water, and measure specific gene expression. There is, however, a need to standardise qPCR protocols if this technique is to be used as an analytical diagnostic tool for routine monitoring. This review focuses on the application of qPCR in the detection of microorganisms in water.
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Affiliation(s)
- Marelize Botes
- Department of Microbiology, University of Stellenbosch, Private Bag XI, Matieland 7602, Stellenbosch, Western Cape 7602, South Africa.
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Singh G, Vajpayee P, Rani N, Jyoti A, Gupta KC, Shanker R. Bio-capture of S. Typhimurium from surface water by aptamer for culture-free quantification. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2012; 78:320-326. [PMID: 22226327 DOI: 10.1016/j.ecoenv.2011.11.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 11/27/2011] [Accepted: 11/28/2011] [Indexed: 05/31/2023]
Abstract
In this study, a DNA aptamer was used to bio-capture Salmonella enterica serovar Typhimurium from surface water collected from highly endemic zone prior to culture-free detection through Molecular-Beacon based real-time PCR assay targeting invA gene. The assay could detect S. Typhimurium cells (1 CFU/PCR or 100 CFU/ml) selectively captured by serovar specific DNA aptamer. The observations indicate that all the water samples (n=40) collected from the river Gomti were contaminated by S. Typhimurium (31400-1 × 10(7) CFU/100 ml). The pre-analytical step in the form of serovar specific DNA aptamer based bio-capture of the bacterial cell was found to enhance the sensitivity of the florescent probe based real-time PCR assay during detection of S. Typhimurium in environmental samples exhibiting natural PCR inhibitors and high background bacterial flora. The assay could be used for the regular monitoring of surface waters for forecasting and management of non-typhoidal Salmonellosis in south Asia.
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Affiliation(s)
- Gulshan Singh
- Environmental Microbiology, CSIR-Indian Institute of Toxicology Research, Post Box 80, Mahatma Gandhi Marg, Lucknow 226001, UP, India
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40
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Patel CB, Vajpayee P, Singh G, Upadhyay RS, Shanker R. Contamination of potable water by enterotoxigenic Escherichia coli: qPCR based culture-free detection and quantification. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2011; 74:2292-2298. [PMID: 21840050 DOI: 10.1016/j.ecoenv.2011.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 07/20/2011] [Accepted: 07/23/2011] [Indexed: 05/31/2023]
Abstract
Tourists visiting to endemic zones may acquire Enterotoxigenic Escherichia coli (ETEC) infection resulting into diarrhea due to consumption of contaminated potable waters. In this study, a qPCR assay (SYBR Green), targeting LT1 and ST1 genes was designed to quantify ETEC in potable waters derived from civic water supply. The assay could detect lowest 1CFU/PCR targeting LT1/ST1 gene from ten-fold diluted culture of the reference strain (E. coli MTCC 723) and is ten-fold more sensitive than the conventional PCR. The quantification of the ETEC in potable waters collected from civic supply of a major city of the northern India exhibiting high flow of tourists reveals that all the sites that ran along sewage line were contaminated by the ETEC. Contamination was due to percolation of sewage. The assay could be used for the regular monitoring of potable water in places exhibiting heavy flow of tourists to prevent ETEC induced diarrhea.
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Affiliation(s)
- C B Patel
- Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Post Box 80, Mahatma Gandhi Marg, Lucknow 226001 UP, India
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41
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Clark ST, Gilbride KA, Mehrvar M, Laursen AE, Bostan V, Pushchak R, McCarthy LH. Evaluation of low-copy genetic targets for waterborne bacterial pathogen detection via qPCR. WATER RESEARCH 2011; 45:3378-3388. [PMID: 21514618 DOI: 10.1016/j.watres.2011.03.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 03/08/2011] [Accepted: 03/27/2011] [Indexed: 05/30/2023]
Abstract
Recent developments in water quality research have highlighted difficulties in accurately predicting the incidence of pathogens within freshwater based on the viability, culturability and metabolic activity of indicator organisms. QPCR-driven assays are candidates to replace standard culture-based methods, however, protocols suitable for routine use have yet to be sufficiently validated. The objective of this study was to evaluate five oligonucleotide primers sets (ETIR, SINV, exoT, VS1 and ipaH2) for their potential applicability in qPCR assays to detect contamination from five waterborne bacterial pathogens (Escherichia coli O157:H7, Salmonella Typhimurium, Campylobacter jejuni, Pseudomonas aeruginosa, and Shigella flexneri). An enrichment-free qPCR protocol was also tested using S. Typhimurium-seeded source water, combining membrane filtration and mechanical, chemical and enzymatic lysis techniques to recover the bacterial cells. All five primer sets were found to have high specificity and sensitivity for the tested organisms. Four of the primers were able to detect pathogen loads as low as 10 cells/mL while 200 cells/mL of C. jejuni were detectable in pure culture. Although sensitivity decreased in an artificially contaminated environmental matrix, it was still possible to detect as few as 10 S. Typhimurium cells without enrichment. The primers and protocols evaluated in this study have demonstrated potential for further validation for possible application alongside traditional indicator techniques.
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Affiliation(s)
- Shawn T Clark
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
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Ram S, Vajpayee P, Dwivedi PD, Shanker R. Culture-free detection and enumeration of STEC in water. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2011; 74:551-557. [PMID: 21459445 DOI: 10.1016/j.ecoenv.2011.01.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Revised: 11/04/2010] [Accepted: 01/30/2011] [Indexed: 05/30/2023]
Abstract
Shiga toxin-producing Escherichia coli (STEC) causes worldwide outbreaks of food and waterborne diseases. Rapid identification of causative agents is critical for early intervention in the case of widespread diarrheal epidemics to prevent mortality. In this study, a Molecular-Beacon targeting stx2 gene (highly associated with human illness) was designed to develop a culture-independent real-time PCR assay for detection and quantification of STEC in water samples. The assay could detect lowest 10 genomic equivalent (GE) of the reference strain (E. coli I.T.R.C.-18) per PCR or 100 GE/mL. The presence of 10(6)CFU/mL of non-pathogenic E. coli DH5α has no impact on sensitivity of the assay. The assay could successfully enumerate STEC in surface water (collected from a sewage impacted river) and potable water samples collected from Lucknow city without prior enrichment. The assay will be useful in pre-emptive monitoring of surface/potable waters to prevent waterborne outbreaks caused by STEC.
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Affiliation(s)
- S Ram
- Environmental Microbiology, Indian Institute of Toxicology Research (C.S.I.R), Post Box 80, Mahatma Gandhi Marg, Lucknow 226001, UP, India
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Comparison of In-house and Commercial Real-time PCR Systems for the Detection of Enterobacteriaceae and their Evaluation Within an Interlaboratory Study Using Infant Formula Samples. FOOD ANAL METHOD 2011. [DOI: 10.1007/s12161-010-9188-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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44
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Aoi R, Shimizu S, Yamazaki K, Sawabe T, Kawai Y. Rapid Quantification of Escherichia coli as an Indicator of Food Contamination Using Fluorescence in situ Hybridization with Filter Cultivation (FISHFC). J JPN SOC FOOD SCI 2011. [DOI: 10.3136/nskkk.58.483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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45
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Langer V, Niessner R, Seidel M. Stopped-flow microarray immunoassay for detection of viable E. coli by use of chemiluminescence flow-through microarrays. Anal Bioanal Chem 2010; 399:1041-50. [DOI: 10.1007/s00216-010-4414-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 11/02/2010] [Accepted: 11/02/2010] [Indexed: 11/27/2022]
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46
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Jyoti A, Ram S, Vajpayee P, Singh G, Dwivedi PD, Jain SK, Shanker R. Contamination of surface and potable water in South Asia by Salmonellae: culture-independent quantification with molecular beacon real-time PCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2010; 408:1256-1263. [PMID: 20035972 DOI: 10.1016/j.scitotenv.2009.11.056] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/18/2009] [Accepted: 11/25/2009] [Indexed: 05/28/2023]
Abstract
Low numbers (15-100CFU) of Salmonella in food or water may pose a public health risk. The management of infections caused by Salmonella spp. during outbreaks or forecasting of contamination of aquatic resources largely depends on rapid, sensitive and accurate diagnostic in few hours. In this study, a real-time PCR assay in Molecular-Beacon format was developed and culture-independent quantitative enumeration of Salmonella spp. in surface and potable water is being reported for the first time from northern part of India. Molecular Beacon was designed in highly conserved region of invA gene (present in wide range of Salmonella serotypes including all subspecies) encoding an essential component of the invasion associated specialized type Ø protein secretion apparatus for detection of Salmonella spp. in water. The assay could detect directly 10 and 1 genomic equivalent of Salmonella typhimurium ATCC 14028 per PCR with detection probability of 100 and 20%, respectively. Further, the assay could detect 10CFU/PCR or more of reference strain (S. typhimurium ATCC 14028) without any enrichment in the presence of 10(8)CFUml(-1) of non-pathogenic E. coli (E. coli DH5alpha) with 100% detection probability. The assay could enumerate Salmonella spp. in surface (n=40) and potable waters (n=10) directly (without enrichment). Results indicate that northern India is at high risk of developing Salmonella borne infections. Further, real-time PCR assay in Molecular Beacon format can be used for identification of critical contamination points in natural water resources and potable water distribution systems, necessary to implement vaccination plan timely for prevention of waterborne outbreaks caused by Salmonella spp.
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Affiliation(s)
- Anurag Jyoti
- Environmental Microbiology, Indian Institute of Toxicology Research (C.S.I.R.), Lucknow, U.P., India
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Evaluation of Lactobacillus sobrius/L. amylovorus as a new microbial marker of pig manure. Appl Environ Microbiol 2009; 76:1456-61. [PMID: 20038684 DOI: 10.1128/aem.01895-09] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Based on a comparison of the dominant microbial populations in 17 pig manure samples and using a molecular typing method, we identified a species, Lactobacillus sobrius and Lactobacillus amylovorus (which now are considered a single species and are designated L. sobrius/amylovorus here), that was consistently found in manure. The aim of the present study was to confirm by real-time PCR the relevance of this species as a marker of pig fecal contamination. The specificity of L. sobrius/amylovorus was evaluated in human and animal DNA extracted from feces. The real-time PCR assay then was applied to water samples, including effluents from urban wastewater treatment plants, runoff water, and rivers. L. sobrius/amylovorus was consistently present in all samples of swine origin: 48 fecal samples, 18 from raw manure and 10 from biologically treated manure at mean concentrations of 7.2, 5.9, and 5.0 log(10) cells/g, respectively. The species was not detected in any of the other livestock feces (38 samples from cattle and 16 from sheep), in the 27 human fecal samples, or in the 13 effluent samples from urban wastewater treatment plants. Finally, L. sobrius/amylovorus was not detected in runoff water contaminated by cattle slurry, but it was quantified at concentrations ranging from 3.7 to 6.5 log(10) cells/100 ml in runoff water collected after pig manure was spread on soil. Among the stream water samples in which cultured Escherichia coli was detected, 23% tested positive for L. sobrius/amylovorus. The results of this study indicate that the quantification of L. sobrius/amylovorus using real-time PCR will be useful for identifying pig fecal contamination in surface waters.
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48
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Comparison of Fecal Indicator Bacteria Densities in Marine Recreational Waters by QPCR. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s12403-009-0019-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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49
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Lavender JS, Kinzelman JL. A cross comparison of QPCR to agar-based or defined substrate test methods for the determination of Escherichia coli and enterococci in municipal water quality monitoring programs. WATER RESEARCH 2009; 43:4967-79. [PMID: 19717179 DOI: 10.1016/j.watres.2009.08.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 07/24/2009] [Accepted: 08/08/2009] [Indexed: 05/15/2023]
Abstract
Molecular methods such as quantitative, real-time polymerase chain reaction (QPCR) are intended to shorten the period between sampling and publicly available results. Cross comparison studies in Racine, WI, USA evaluated QPCR against agar-based (US EPA Method 1600) and defined substrate (IDEXX Colilert-18) methods for the detection and quantification of Escherichia coli and enterococci in a variety of aqueous environments (wastewater, stormwater, and surface water). Regulatory outcomes were also compared based on choice of indicator and method. Positive correlation was seen between QPCR cell equivalents and viable cells through the wastewater treatment process and in all surface water samples (river or freshwater bathing beach) but not in direct stormwater discharge. For surface water samples, correlation improved with the application of a site-specific corrective factor, with regulatory action correctly predicted 98% of the time at bathing beaches. This study suggests the potential utility of QPCR for certain water quality monitoring applications.
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Affiliation(s)
- Jennifer S Lavender
- Health Department, City of Racine, 730 Washington Avenue, Racine, WI 53403, USA.
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50
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Development and application of quantitative-PCR tools for subgroups of the Roseobacter clade. Appl Environ Microbiol 2009; 75:7542-7. [PMID: 19801463 DOI: 10.1128/aem.00814-09] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Specific SYBR green-based quantitative-PCR assays targeting conserved regions in the 16S-23S rRNA internal transcribed spacer regions were developed for five subgroups of the environmentally abundant and biogeochemically active Roseobacter clade of marine bacteria. The assays were applied to field samples demonstrating their utility in investigations of abundant Roseobacter group phylotypes in the environment.
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