Investigation into the microbial contamination in a spring water distribution system, Western Cape, South Africa
30 Sep 2011-African Journal of Microbiology Research (Academic journals)-Vol. 5, Iss: 20, pp 3200-3214
TL;DR: This paper aims to demonstrate the efforts towards in-situ applicability of EMMARM, which aims to provide real-time information about concrete mechanical properties such as E-modulus and compressive strength.
Abstract: National Research Foundation (NRF) and Cape
Peninsula University of Technology (CPUT) for financial
support.
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TL;DR: An analysis of 39 whole-genome sequences comprising three Comamonas species from aquatic environments in South Australia that were recovered on media supplemented with carbapenems makes several key observations, including the identification of a subset of C. denitrificans isolates that harbored genomic islands encodingcarbapenemase blaGES-5 or extended-spectrum β-lactamases blaOXA alleles.
Abstract: Antimicrobial resistance (AMR) poses a global public health threat, and the increase in resistance to “last-resort drugs,” such as carbapenems, is alarming. Wastewater has been flagged as a hot spot for AMR evolution. Comamonas spp. are among the most common bacteria in wastewater and play a role in its bioaugmentation. ABSTRACT Comamonas spp. are Gram-negative bacteria that catabolize a wide range of organic and inorganic substrates. Comamonas spp. are abundant in aquatic and soil environments, including wastewater, and can cause opportunistic infections in humans. Because of their potential in wastewater bioaugmentation and bioremediation strategies, the identification of Comamonas species harboring genes encoding carbapenemases and other clinically important antibiotic resistance genes warrant further investigation. Here, we present an analysis of 39 whole-genome sequences comprising three Comamonas species from aquatic environments in South Australia that were recovered on media supplemented with carbapenems. The analysis includes a detailed description of 33 Comamonas denitrificans isolates, some of which carried chromosomally acquired blaGES-5, blaOXA, and aminoglycoside resistance (aadA) genes located on putative genomic islands (GIs). All blaGES-5- and blaOXA-containing GIs appear to be unique to this Australian collection of C. denitrificans. Notably, most open reading frames (ORFs) within the GIs, including all antimicrobial resistance (AMR) genes, had adjacent attC sites, indicating that these ORFs are mobile gene cassettes. One C. denitrificans isolate carried an IncP-1 plasmid with genes involved in xenobiotic degradation and response to oxidative stress. Our assessment of the sequences highlights the very distant nature of C. denitrificans to the other Comamonas species and its apparent disposition to acquire antimicrobial resistance genes on putative genomic islands. IMPORTANCE Antimicrobial resistance (AMR) poses a global public health threat, and the increase in resistance to “last-resort drugs,” such as carbapenems, is alarming. Wastewater has been flagged as a hot spot for AMR evolution. Comamonas spp. are among the most common bacteria in wastewater and play a role in its bioaugmentation. While the ability of Comamonas species to catabolize a wide range of organic and inorganic substrates is well documented, some species are also opportunistic pathogens. However, data regarding AMR in Comamonas spp. are limited. Here, through the genomic analyses of 39 carbapenem-resistant Comamonas isolates, we make several key observations, including the identification of a subset of C. denitrificans isolates that harbored genomic islands encoding carbapenemase blaGES-5 or extended-spectrum β-lactamase blaOXA alleles. Given the importance of Comamonas species in potential wastewater bioaugmentation and bioremediation strategies, as well as their status as emerging pathogens, the acquisition of critically important antibiotic resistance genes on genomic islands warrants future monitoring.
6 citations
Dissertation•
01 Jan 2013
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Book•
19 Aug 1996
TL;DR: In this paper, the authors describe the characteristics of Predominant Microorganisms in Food and their roles in the development of Food Microbiology and Food Microbiological Quality of Foods.
Abstract: Introduction to Microbes in Foods History and Development of Food Microbiology Introduction Discovery of Microorganisms Where are they Coming From? What are their Functions? Development of Early Food Microbiology (Before A.D. 1900) Food Microbiology: Current Status Food Microbiology and Food Microbiologists Characteristics of Predominant Microorganisms in Food Introduction Classification of Microorganisms Nomenclature Morphology and Structure of Microorganisms in Foods Important Microorganisms in Food Important Viruses Important Bacterial Genera Important Bacterial Groups in Foods Sources of Microorganisms in Foods Introduction Predominant Microorganisms in Different Sources Normal Microbiological Quality of Foods and Its Significance Introduction Raw and Ready-to-eat Meat Products Raw and Pasteurized Milk Shell Egg and Liquid Egg Fish and Shellfish Vegetables, Fruits, and Nuts Cereal, Starches, and Gums Canned Foods Sugars and Confectioneries Soft Drinks, Fruit and Vegetable Drinks, Juices, and Bottled Water Mayonnaise and Salad Dressings Spices and Condiments Microbial Foodborne Diseases Microbial Growth Characteristics Introduction Microbial Reproduction or Growth Nature of Microbial Growth in Food Factors Influencing Microbial Growth in Food Introduction Intrinsic Factors or Food Environment Extrinsic Factors Microbial Metabolism of Food Components Introduction Respiration and Fermentation during Growth Metabolism of Food Carbohydrates Degradation of Polysaccharides Microbial Sporulation and Germination Introduction Mold Spores Yeast Spores Bacterial Spores Importance of Spores in Food Beneficial Uses of Microorganisms in Food Microbial Stress Response in the Food Environment Introduction Stress Adaptation Sublethal Stress and Injury Viable-but-Nonculturable Proponent Views Microorganisms Used in Food Fermentation Introduction Microbiology of Fermented Foods Lactic Starter Cultures Other Starter Cultures Yeasts and Molds Biochemistry of Some Beneficial Traits Introduction Mechanisms of Transport of Nutrients Transport and Metabolism of Carbohydrates Transport and Metabolism of Proteinaceous Compounds and Amino Acids Transport and Metabolism of Lipid Compounds Genetics of Some Beneficial Traits Introduction Plasmids and Plasmid-Linked Traits in Starter-Culture Bacteria Gene Transfer Methods in Starter-Culture Bacteria Gene Cloning Genome Mapping and Sequencing Starter Cultures and Bacteriophages Introduction History Concentrated Cultures Starter-Culture Problems Yeast and Mold Cultures Microbiology of Fermented Food Introduction General Method of Production Fermented Dairy Products Fermented Meat Products Fermented Vegetable Products Intestinal Beneficial Bacteria Introduction Microbiology of the Human GI Tract Important Characteristics of Beneficial Bacteria Beneficial Effects of Probiotics Some Aspects to Consider Current Developments Food Biopreservatives of Microbial Origin Introduction Viable Cells of Lactic Acid Bacteria as Preservatives Organic Acids, Diacetyl, Hydrogen Peroxide, and Reuterine as Food Preservatives Bacteriocins of Lactic Acid Bacteria as Food Preservatives Yeast Metabolites as Preservatives Food Ingredients and Enzymes of Microbial Origin Introduction Microbial Proteins and Food Additives Microbial enzymes in Food processing Microbial Food Spoilage Important Factors in Microbial Food Spoilage Introduction Sequence of Events Significance of Microorganisms Some Important Food Spoilage Bacteria Significance of Foods Spoilage of Specific Food Groups Introduction Fresh and Ready-To-Eat Meat Products Eggs and Egg Products Fish, Crustaceans, and Mollusks Milk and Milk Products Vegetables and Fruits Soft Drinks, Fruit Juices and Preserves, and Vegetable Juices Cereals and their Products Liquid Sweeteners and Confectioneries Mayonnaise, Salad Dressings, and Condiments Fermented Foods Canned Foods New Food Spoilage Bacteria in Refrigerated Foods Microorganisms that Grow in Refrigerated Foods (Psychotrophs) Popularity of Refrigerated Foods Microbiological Problems Incidence of Spoilage of Vacuum-Packaged Refrigerated Food Food Spoilage by Microbial Enzymes Introduction Characteristics of Heat-Stable Enzymes of Psychotrophic Bacteria Spoilage of Foods with Heat-Stable Microbial Enzymes Spoilage of Foods by Microbial Enzymes at Low Temperature Indicators of Microbial Food Spoilage Introduction Microbiological Criteria Chemical Criteria Assay of Heat-Stable Enzymes Microbial Foodborne Diseases Important Facts in Foodborne Diseases Introduction Human Gastrointestinal Disorder Epidemiological Aspects Current Trends Foodborne Intoxications Introduction Staphylococcal Intoxication Botulism Mycotoxicosis Foodborne Infections Introduction Salmonellosis by Salmonella enterica Listeriosis by Listeria monocytogenes Pathogenic Escherichia coli Shigellosis (Bacillary Dysentery) by Shigella spp Campylobacteriosis by Campylobacter spp Yersiniosis byYersinia enterocolitica Gastroenteritis by Vibrio spp Enteric Viruses Other Foodborne Infections Foodborne Toxicoinfections Introduction Clostridium perfringens Gastroenteritis Bacillus cereus Gastroenteritis Cholera Escherichia coli Gastroenteritis Opportunistic Pathogens, Parasites, and Algal Toxins Introduction Opportunistic Pathogens Biogenic Amines Algal Toxins Parasites New and Emerging Foodborne Pathogens Introduction Associated Factors Miscellaneous Factors Other Emerging Foodborne Pathogens of Concern Indicators of Bacterial Pathogens Introduction Criteria for Ideal Indicators Coliform Group Enterobacteriaceae Group Enterococcus Group Control of Microorganisms in Foods Control of Access (Cleaning and Sanitation) Introduction Objectives of Sanitation Factors to Consider Control by Physical Removal Control by Heat Introduction Objectives Mechanism of Thermal Inactivation Influencing Factors Nature of Food Mathematical Expressions Methods Control by Low Temperature Introduction Objectives Mechanisms of Cold Induced Inactivation Influencing Factors Methods Control by Reduced Water Activity Introduction Objectives Mechanism of Action Influencing Factors Nature of Microorganisms Methods Control by Low pH and Organic Acids Introduction Objectives Mechanisms of Antimicrobial Action Influencing Factors Acids Used Control by Modified Atmosphere (or Reducing O-R Potential) Introduction Objectives Mechanism of Action Influencing Factors Methods Control by Antimicrobial Preservatives Introduction Objectives Influencing Factors Examples of Antimicrobial Preservatives H2O2 Control by Irradiation Introduction Objectives Mechanisms of Antimicrobial Action Influencing Factors Methods Control by Novel Processing Technologies Introduction Summary of Processing Methods Pulsed Electric Field Hydrostatic Pressure Processing Control by a Combination of Methods (Hurdle Concept) Introduction Mechanisms of Antimicrobial Action Current Status Microbial Detection and Food Safety Conventional and Biosensor Based Detection Methods for Microorganisms in Food and Food Environment Introduction Methods Used Standard and Recommended Methods Sampling for Microbial Analysis Quantitative Methods for Microbial Enumeration in Foods Qualitative Methods to Isolate Microorganisms in Foods Test for Bacterial Toxins in Foods Rapid Methods and Automation Biosensors for Pathogen Detection Appendix A: Microbial Attachment to Food and Equipment Surfaces Importance Mechanisms of Attachment Influencing Factors Control Measures Appendix B: Predictive Modeling of Microbial Growth in Food Importance Traditional Methods Predictive Microbiology Appendix C: Regulatory Agencies Monitoring Microbiological Safety of Foods in the United States Food Safety Regulations The Agencies Appendix D: Hazard Analysis Critical Control Points Introduction HACCP Principle of the NACMCF Index
627 citations
TL;DR: Although all NLV strains identified were closely related, three mineral water brand-specific clusters could be identified for both primer systems by sequencing and levels of contamination in positive mineral water samples were estimated to be in the range of 10 to 100 genomic equivalents per liter.
Abstract: In a recent study, RNA with nucleotide sequeces specific for “Norwalk-like viruses” (NLV) was detected in 11 different brands of European mineral waters. To clarify this finding, a 1-year monitoring study was conducted. Samples of three European brands of mineral water without gas were monitored weekly by reverse transcriptase PCR using generic and genogroup-specific oligonucleotides. Additional analyses were performed to investigate a possible correlation between NLV sequence contamination and mineral water lot numbers, the long-term stability (persistence) of NLV sequences in mineral water, and the level of contamination. NLV sequences were detected in 53 of 159 samples analyzed (33%) and belonged entirely to genogroup II. Although all NLV strains identified were closely related, three mineral water brand-specific clusters could be identified for both primer systems by sequencing. Analyses of second samples from lots previously shown to be positive for NLV sequences gave corresponding results in 45 of 53 cases (85%) (within a six-pack). NLV persistence was tested by analyzing 10 positive samples after 6 and 12 months of storage in darkness at room temperature. After 6 months, all samples remained positive; after 12 months, 9 of 10 samples were still positive for NLV sequences. No NLV sequences could be detected by analysis of 0.1-liter aliquots of 53 samples shown to be positive by testing of 1-liter volumes. Based on this fact and a test sensitivity of approximately 10 viral units, levels of contamination in positive mineral water samples were estimated to be in the range of 10 to 100 genomic equivalents per liter.
151 citations
"Investigation into the microbial co..." refers background in this paper
...Beuret et al. (2002) monitored three brands of natural mineral waters in Europe over a one year period to investigate and identify the microbial flora present. Norovirus sequences were isolated from three leading European brands of still mineral water, during the course of this investigation. Research by Leclerc (2002) on the microbiological safety of bottled water, identified the major species of bacteria associated with natural mineral water as Pseudomonas fluorescent species, Pseudomonas non-fluorescent species, Acinetobacter, Alcaligenes, Comamonas spp....
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...Beuret et al. (2002) monitored three brands of natural mineral waters in Europe over a one year period to investigate and identify the microbial flora present....
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TL;DR: On a continuing basis, the management of microbial risks has to rely on assessment of the heterotrophic plate count and on detection of marker organisms, i.e. the classic fecal contamination indicators that have to be absent, and vulnerability indicators for which the occurrence should be as low as possible.
Abstract: Natural mineral water originates from groundwater, an oligotrophic ecosystem where the level of organic matter is low and of a very limited bioavailability. The bacterial populations that evolve in these ecosystems are heterotrophic and in starvation–survival state resulting from an insufficient amount of nutrients; for this reason they enter a viable but non-culturable state. After bottling, the number of viable counts increases rapidly, attaining 104–105 colony-forming units ml−1 within 3–7 days. These bacterial communities, identified by culture or with specific probes, are primarily aerobic, saprophytic, Gram-negative rods. Groundwater sources for natural mineral waters are selected such that they are not vulnerable to fecal contamination. Ecological data, especially the diversity and physiological properties of bacterial communities, are essential together with epidemiological studies in order to perform a risk analysis for natural mineral waters. On a continuing basis, the management of microbial risks has to rely on assessment of the heterotrophic plate count and, more specially, on detection of marker organisms, i.e. the classic fecal contamination indicators that have to be absent, and vulnerability indicators for which the occurrence should be as low as possible. It is also recommended to search regularly, but not routinely, for viral and protozoan pathogens.
150 citations
TL;DR: The primary sequences of the V3 and V6 regions of the 16S rRNA gene of pathogenic and non‐pathogenic strains of Escherichia coli were determined and compared with those obtained for a number of reference strains which belong to the family Enterobacteriaceae.
Abstract: The primary sequences of the V3 and V6 regions of the 16S rRNA gene of pathogenic and non-pathogenic strains of Escherichia coli were determined and compared with those obtained for a number of reference strains which belong to the family Enterobacteriaceae. Three oligonucleotide primers 16E1, 16E2 and 16E3 were designed and used in the polymerase chain reaction to identify specifically all E. coli isolates. When 16E1, 16E2 and 16E3 were used as primers for the identification of E. coli cells present in tap, underground and pond waters, as low as 1 cfu 100 ml-1 of water could be detected if an 8 h pre-culture step was performed prior to the PCR reaction.
105 citations
"Investigation into the microbial co..." refers methods in this paper
...Tsen et al. (1998) utilised PCR to select regions of the Escherichia coli 16 S ribosomal ribonucleic acid (rRNA) gene to detect these cells in water....
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Book•
01 Jul 1986
TL;DR: In this article, the authors present a self-contained textbook for one-year courses in analysis of variance and regression, with omissions for a onesemester course in statistical analysis.
Abstract: written with a dual purpose. First, it was intended to be a self-contained textbook suitable for a one-year course, or, with omissions, for a onesemester course in analysis of variance and regression. Second, it was intended to be useful as a reference book. In preparing a second edition, we have kept these two purposes in mind and have added a third. We wish the book to be helpful to the ever-increasing number of investigators who, with only a year or so of statistical training, are performing sophisticated statistical analyses on computers. (p. v)
85 citations
"Investigation into the microbial co..." refers background or methods in this paper
...In a random survey of bottled water conducted in South Africa by Ehlers et al. (2004), heterotrophic plate counts ranging from 1....
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...Repeated measures analysis of variance (ANOVA) [RMA] were performed on all data obtained as outlined in Dunn and Clark (1987) using StatisticaTM....
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...In a random survey of bottled water conducted in South Africa by Ehlers et al. (2004), heterotrophic plate counts ranging from 1.1 x 10(2) to 5.4 x 10(2) cfu/ml were recorded. It was concluded that the presence of these high numbers were due to the natural microbial flora present in the source water and could thus be used to indicate the level of disinfection of the distribution and bottling system (Leclerc and Moreau, 2002). Flow cytometry is used to sort and measure different types of cells by the fluorescent labelling of markers on the surface of the cell (Javois, 1999). The addition of fluorescent beads in conjunction with the Live/Dead BacLightTM viability probe allows for the enumeration of total bacteria in the water samples. Paulse et al. (2007) assessed various enumeration techniques to investigate the planktonic bacterial population in the Berg River, Western Cape, South Africa....
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...Repeated measures analysis of variance (ANOVA) [RMA] were performed on all data obtained as outlined in Dunn and Clark (1987) using Statistica....
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