Using ultrafiltration to concentrate and detect Bacillus anthracis, Bacillus atrophaeus subspecies globigii, and Cryptosporidium parvum in 100-liter water samples

A strategy that uses ultrafiltration (UF) to concentrate microorganisms from water samples has been developed and tested. This strategy was tested using 100-liter water samples with volume reduction achieved through ultrafiltration and recycling the microorganisms of interest through a retentate vessel, rather than returning them to the sample container, where they might pose an incremental hazard to sample takers or the environment. Three protocols based on this strategy were tested. The first protocol entailed sample volume reduction and collection of the final reduced sample. The second and third protocols both incorporated pretreatment of the filter and fluid lines with a solution to prevent microorganisms from adhering. In the second protocol, the filter was back flushed with a surfactant solution to recover microorganisms. The third protocol used recirculation of a surfactant solution to recover microorganisms. Tests were undertaken using 100-liter water samples spiked with approximately 100 or 1000 microorganisms (1 or 10 per liter). Test microorganisms included Bacillus anthracis Sterne strain, Bacillus atrophaeus subsp. globigii, and Cryptosporidium parvum. The first protocol had significantly lower recovery than the other two. Back flushing resulted in higher recovery than forward flushing, but the difference was not statistically significant.     

Direct quantitation and detection of salmonellae in biological samples without enrichment, using two-step filtration and real-time PCR

A new two-step filtration protocol followed by a real-time PCR assay based on SYBR green I detection was developed to directly quantitate salmonellae in two types of biological samples: i.e., chicken rinse and spent irrigation water. Four prefiltration filters, one type of final filter, and six protocols for recovery of salmonellae from the final filter were evaluated to identify an effective filtration protocol. This method was then combined with a real-time PCR assay based on detection of the invA gene. The best results were obtained by subsequent filtration of 100 ml of chicken rinse or 100 ml of spent irrigation water through filters with pore diameters of >40 mum to remove large particles and of 0.22 microm to recover the Salmonella cells. After this, the Salmonella cells were removed from the filter by vortexing in 1 ml of physiological saline, and this sample was then subjected to real-time quantitative PCR. The whole procedure could be completed within 3 h from sampling to quantitation, and cell numbers as low as 7.5 x 10(2) CFU per 100-ml sample could be quantified. Below this limit, qualitative detection of concentrations as low as 2.2 CFU/100 ml sample was possible on occasion. This study has contributed to the development of a simple, rapid, and reliable method for quantitation of salmonellae in food without the need for sample enrichment or DNA extraction.     

Loss of pico- and nanoplankton cells during concentration by tangential flow filtration

The efficiency of a tangential flow filtration device to concentratepico- and nanoplankton particles in sea water uniformly overa range of concentrations was evaluated. To calculate the expenmentalrecovery rates for each concentration factor, we measured theincrease in chlorophyll concentration, number of total particles(Coulter counter) and number of autotrophic cells (flow cytometry).The experimental recovery rates for each stage of volume reductionin the concentration process were expressed as percentages ofthe expected theoretical values. Significant losses of cellularmaterial (low recovery rates) occurred between the retentateseawater tank and the seawater filtrate tank. Similar lossesoccurred in repetitive closed-circuit recirculation experimentswhen the circulating volume of sea water was kept constant.The cause of the apparent losses of material appeared to bemechanical fragmentation of organisms during the pumping andfiltering stages; however, experiments with latex beads showedthat most of the missing beads were retained within the filtrationelements. The low efficiencies and extremely varied recoveryrates of tangential flow filtrations measured under the experimentalconditions and for the different types of particles used inthis work preclude its use for quantitative concentrations ofnatural assemblages of particulate material in sea water.     

Comparison of gauze swabs and membrane filters for isolation of Campylobacter spp. from surface water.

The epidemiology of Campylobacter jejuni indicates that waterborne transmission is important; the organism has been isolated from seawater, fresh water, and estuarine sites. Membrane filtration, with and without use of an enrichment broth, has been the most common method for isolating C. jejuni from water. We evaluated two methods for isolating C. jejuni from water: membrane filtration and gauze filtration. The membrane filters evaluated included 0.22- and 0.45-micron-pore Millipore filters (Millipore Corp., Bedford, Mass.), 0.2- and 0.4-micron-pore Nuclepore filters (Nucleopore Corp., Pleasanton, Calif.), and a 0.45-micron-pore Zetapor filters (AMF Cuno, Meridian, Conn.). The gauze filters included both Moore and Spira swabs. Of the membrane filters evaluated, the 0.45-micron-pore Millipore and Zetapor filters were the most sensitive for recovery of C. jejuni from seeded waters. The 0.45-micron-pore Millipore filter placed in Oosterom broth was better for recovery of C. jejuni from seeded stationary surface waters than either the Spira or Moore swab. However, the 0.45-micron-pore Millipore filter placed on a plate or in enrichment broth was equivalent to the Spira gauze swab when used to examine water from Atlanta area streams. C. jejuni organisms were isolated from 9 of 24 surface water samples representing 5 of 12 streams.     

Comparison of gauze swabs and membrane filters for isolation of Campylobacter spp. from surface water

The epidemiology of Campylobacter jejuni indicates that waterborne transmission is important; the organism has been isolated from seawater, fresh water, and estuarine sites. Membrane filtration, with and without use of an enrichment broth, has been the most common method for isolating C. jejuni from water. We evaluated two methods for isolating C. jejuni from water: membrane filtration and gauze filtration. The membrane filters evaluated included 0.22- and 0.45-micron-pore Millipore filters (Millipore Corp., Bedford, Mass.), 0.2- and 0.4-micron-pore Nuclepore filters (Nucleopore Corp., Pleasanton, Calif.), and a 0.45-micron-pore Zetapor filters (AMF Cuno, Meridian, Conn.). The gauze filters included both Moore and Spira swabs. Of the membrane filters evaluated, the 0.45-micron-pore Millipore and Zetapor filters were the most sensitive for recovery of C. jejuni from seeded waters. The 0.45-micron-pore Millipore filter placed in Oosterom broth was better for recovery of C. jejuni from seeded stationary surface waters than either the Spira or Moore swab. However, the 0.45-micron-pore Millipore filter placed on a plate or in enrichment broth was equivalent to the Spira gauze swab when used to examine water from Atlanta area streams. C. jejuni organisms were isolated from 9 of 24 surface water samples representing 5 of 12 streams.     

Share the details of your experimental methods

Incomplete methods sections have made it difficult for researchers to replicate and build on the work of others, contributing to problems in reproducibility. It is important to increase the level of detail in our methods sections and to share step-by-step protocols in protocol repositories or journals. Request a Protocol is a new feature in Molecular Biology of the Cell that allows readers to request detailed protocols directly from the methods section of the research article, with links between the protocols and the research articles, and has the potential to improve research reproducibility and help everyone design and execute robust life science experiments.     

Assessment of the tolerance to Fe,Cu and Zn of a sulfidogenic sludge generated from hydrothermal vents sediments as a basis for its application on metals precipitation

Molecular Biology Reports - A paramour factor limiting metal-microorganism interaction is the metal ion concentration, and the metal precipitation efficiency driven by microorganisms is sensitive...     

The filtration rate of the zebra mussel Dreissena polymorpha used for water quality assessment in Dutch rivers

The effects of contaminated river water on the filtration rate of zebra mussels from a clean reference site were studied. After a 48-h exposure period to filtered water from the rivers Rhine, Meuse and Amstel (The Netherlands), the filtration rate was measured. It was demonstrated that water from contaminated locations inhibited the filtration rate. Inhibition was higher during low water levels in the rivers Rhine and Meuse than during high water levels, suggesting that contaminants are diluted during high water levels. It is concluded that the shortterm filtration assay with D. polymorpha can be used for assessing water quality.     

Enumeration and isolation of viral particles from oligotrophic marine environments by tangential flow filtration.

A method for concentrating, enumerating and isolating viral particles from marine water samples was developed and evaluated. The method consists of a concentration step by a tangential flow filtration (TFF) system, ultrafiltration by centrifugal concentrator, and visualization by transmission electron microscopy (TEM). This procedure allows to reduce volumes of ca. 21 of seawater to 10-20 microliters, which can be dispensed on electron microscopy grids to count total viral particles. This method allows the recovery of small numbers of viral particles from oligotrophic seawater samples, in which viral numbers ranged from 10(5) to 10(6) viral particles/ml. The tangential flow filtration system was evaluated as quantitative technique using suspensions of two different bacteriophages (T6 and phi X174) in autoclaved seawater. Recovery rates varied depending on both the viral morphology and flow rate; recovery percentages reached 117.4% for T6 and 60.6% for phi X174 using low flow rate.     

Precision and accuracy of recovery of Legionella pneumophila from seeded tap water by filtration and centrifugation.

Determination of the concentration of Legionella pneumophila in environmental water sites may be useful for the prediction of the risk of a particular site's causing Legionnaires' disease as well as for experimental studies of environmental growth or remediation. The precision and accuracy of recovery of two different L. pneumophila strains from seeded tap water samples were studied, with either filtration or centrifugation used to concentrate the bacteria. L. pneumophila grown on BCYE alpha agar or in Acanthamoeba castellanii was used to seed sterile tap water. Water samples were then either filtered (0.2-microns pore size) or centrifuged. An average of 53% (95% confidence interval [CI], 47 to 58%; n = 45) of the seeded L. pneumophila organisms were recovered by filtration with flat polycarbonate membranes. This recovery was significantly higher (P < 0.01) than that obtained by filtration with cast membranes (mean, 13%; 95% CI, 11 to 38%; n = 4) or by centrifugation at 3,800 x g for 30 min (mean, 14%; 95% CI, 2 to 25%; n = 9) or at 8,150 x g for 15 min (mean, 32%; 95% CI, 28 to 36%; n = 19). Recovery of L. pneumophila was not significantly different whether the bacteria were grown on plates or in amoebae. Use of a selective medium did not decrease the recovery efficiency, but preplating acid treatment of specimens caused an approximately 30% bacterial loss.(ABSTRACT TRUNCATED AT 250 WORDS)     

An improved sampling protocol for analysis of intracellular metabolites in Mortierella alpina

Sampling of intracellular metabolites in Mortierella alpina was investigated as part of a metabolomics study. After comparison of four sampling protocols, rapid filtration of the culture using a laboratory-made nylon filter and absorbent gauze under normal pressure followed by quenching in liquid N₂ and grinding (the improved protocol) was the most effective. Rapid filtration under normal pressure decreased intracellular metabolites leakage and subsequent grinding of cells contributed to intracellular metabolites extraction. The above quenching method together with 75?% (v/v) ethanol, buffered with 60?mM HEPES, at 80?°C for 3?min is therefore suitable for sampling intracellular metabolites in M. alpina.     

Assessment of the efficacy of Sephadex G-15 filtration of bovine spermatozoa for cryopreservation

Semen from five dairy AI bulls was split-filtered through a Sephadex G-15 filter and frozen in a Tris-citric acid buffer egg yolk-based extender. The effect of filtration was studied morphologically for individual sperm abnormalities. Computer-assisted sperm analysis (CASA) was used for motility and sperm motion assessment. Flow cytometry was used to disclose sperm viability (SYBR-14/PI), mitochondrial membrane potential (Mitotracker Deep Red/SYBR 14), acrosome integrity (SYBR 14/PE-PNA/PI), plasma membrane stability (Merocyanine 540/YO-PRO 1/Hoechst 333342), and chromatin stability (acridine orange staining). Filtration significantly reduced the concentration of recovered spermatozoa (P < 0.01), but improved semen quality, reducing the number of spermatozoa with various forms of morphological defects. Filtration also affected percentages of sperm motility after equilibration and after freezing/thawing. Sperm motion characteristics were, however, not significantly affected by filtration at any stage of the cryopreservation protocol, including post-extension, equilibration, or freezing/thawing. Filtration enhanced sperm viability after thawing (P < 0.05), but had no significant effect (P > 0.05) on recovery of spermatozoa with high mitochondrial potential, intact acrosomes, or preserved sperm chromatin structure. Sperm plasma membrane stability was also not affected by the filtration method used (P > 0.05). It can be concluded that filtration effectively separates weaken or abnormal spermatozoa in pre-freezing semen samples and therefore the procedure could be recommended to improve post-thaw sperm viability of selected, fertile sires.     

An optimized protocol for the identification of diatoms,flagellated algae and pathogenic protozoa with phylochips

In the past decade, molecular probe‐based methods have proved successful in improving both the efficiency and accuracy of the identification of microorganisms, especially those that are devoid of distinct morphological features. However until recently, these methods had the major drawback of being limited to the identification of only one or just a few species at a time. With the use of DNA microarrays, it is possible to identify large numbers of taxa on a single‐glass slide, the so‐called phylochip. There are numerous microarray protocols in the literature. These protocols share the same principles, but vary in details, e.g. labelling approach or detergent concentration in the washing buffer. In this study, we show that even small variations in hybridization protocols can have a strong impact on the outcome of the microarray hybridization. An optimized protocol for species identification on phylochips is presented. The optimized protocol is the result of a joined effort of three laboratories to develop phylochips for microbial species identification.     

Rapid separation and quantitation of mixed microorganisms by filtration and bioluminescence

A membrane filtration/bioluminescence system was developed for the differentiation and quantitation of mixed populations of microorganisms. Samples containing microorganisms were filtered through two membrane filters of descending pore size. The microorganisms retained on the filter contain ATP that can be extracted and measured on the filter via the firefly luciferase-luciferin bioluminescence assay. Results, obtained in less than 20 min, show a good correlation (r greater than or equal to 0.95) between the light produced and the number of organisms in the sample. Using these techniques, Escherichia coli can be separated from yeast or mold and measured in samples containing both microorganisms. When lysostaphin is used to selectively lyse Staphylococci on the filter, the specific quantification of these bacteria among other microorganisms can also be accomplished. The filtration/bioluminescence technique offers the potential of being a rapid and sensitive method to differentiate and detect microorganisms, by selective sizing or lysing, in a variety of samples.     

A review of resources of the Internet site "Practical Molecular Biology"]

In 2000, in the middle of September, the Russian Web site Practical Molecular Biology (http://molbiol.edu.ru) was opened. The main tasks of the project are (i) distribution of experimental work experience among Russian and foreign laboratories, and (ii) organization of an information database in Russian for researchers connected with molecular biology or medicine.     

Membrane filtration of food suspensions.

Factors affecting the membrane filtration of food suspensions were studied for 58 foods and 13 membrane filters. Lot number within a brand, pore size (0.45 or 0.8 micrometer), and time elapsed before filtration had little effect on filterability. Brand of membrane filter, flow direction, pressure differential, age (microbiological quality) of the food, duration of the blending process, temperature, and concentration of food in the suspension had significant and often predictable effects. Preparation of suspensions by Stomacher (relative to rotary blender) addition of surfactant (particularly at elevated temperature) and prior incubation with proteases sometimes had dramatic effects of filterability. In contrast to popular opinion, foods can be membrane filtered in quantities pertinent to the maximums used in conventional plating procedures. Removal of growth inhibitors and food debris is possible by using membrane filters. Lowering of the limits of detection of microorganisms by concentration on membrane filters can be considered feasible for many foods. The data are particularly relevant to the use of hydrophobic grid-membrane filters (which are capable of enumerating up to 9 X 10(4) organisms per filter) in instrumented methods of food microbiological analysis.     

Chronic kidney disease and automatic reporting of estimated glomerular filtration rate: a position statement

The systematic staging of chronic kidney disease (CKD) by glomerular filtration measurement and proteinuria has allowed the development of rational and appropriate management plans. One of the barriers to early detection of CKD is the lack of a precise, reliable and consistent measure of kidney function.The most common measure of kidney function is currently serum creatinine concentration. It varies with age, sex, muscle mass and diet, and interlaboratory variation between measurements is as high as 20%.The reference interval for serum creatinine concentration includes up to 25% of people (particularly thin, elderly women) who have an estimated glomerular filtration rate (eGFR) that is significantly reduced (< 60 mL/min/1.73 m). The recent publication of a validated formula (MDRD) to estimate GFR from age, sex, race and serum creatinine concentration, without any requirement for measures of body mass, allows pathology laboratories to "automatically" generate eGFR from data already acquired. Automatic laboratory reporting of eGFR calculated from serum creatinine measurements would help to identify asymptomatic kidney dysfunction at an earlier stage. eGFR correlates well with complications of CKD and an increased risk of adverse outcomes such as cardiovascular morbidity and mortality. We recommend that pathology laboratories automatically report eGFR each time a serum creatinine test is ordered in adults. As the accuracy of eGFR is suboptimal in patients with normal or near-normal renal function, we recommend that calculated eGFRs above 60 mL/min/1.73 m be reported by laboratories as "> 60 mL/min/1.73 m", rather than as a precise figure.     

Comparative study of membrane filtration and enrichment media for the isolation and enumeration of Pseudomonas aeruginosa from sewage, surface water, and swimming pools

The recovery of Pseudomonas aeruginosa on several selective culture media was tested using raw sewage and secondary sewage effluent samples as well as spiked chlorinated imitation swimming water and samples from whirlpools. mPA-medium B gave good recovery of both vital and chlorine-injured P. aeruginosa and selectivity was greater than 90% when analysing whirlpool samples. It is therefore the medium recommended for examination of chlorinated swimming pools. When analysing sewage polluted water with the mPA-B medium, reduced selectivity was noted from low verification rates and from overgrowth by competitive flora. A modified medium (mPA-D; addition of cetrimide, omission of sulphapyridine and actidione) was more selective and sufficiently recovered noninjured cells. Chlorine-injured cells were completely inhibited, however. C-390 (9-chloro-9-(4-diethylaminophenyl)-10-phenylacridan) was confirmed to be highly selective for P. aeruginosa when used in spread plates at a concentration of 30 micrograms/mL; P. aeruginosa was slightly inhibited. However, the medium could not be used with conventional membrane filtration techniques, because cellulose ester filters interfered with the selective action of C-390. Selectivity could be improved by using Gelman Tuffryn (polysulphone) filters and increasing the C-390 concentration to 120 micrograms/mL. At this concentration, however, the medium was strongly inhibitory to P. aeruginosa; resuscitation only partially improved recovery. Two other membrane filtration media were tested. Both cetrimide - nalidixic acid agar and Drake's medium No. 19 were inhibitory to chlorine-injured cells. Several types of membrane filters were tested and there was little difference between them.(ABSTRACT TRUNCATED AT 250 WORDS)     

Mechanisms of neonatal increase in glomerular filtration rate

To investigate the mechanisms responsible for the neonatal increase in glomerular filtration rate (GFR), renal function studies (whole kidney and micropuncture) were carried out in anesthesized fetal sheep (133-140 days gestation; term = 150 days) and lambs (12-18 days). Fetuses were delivered and placed in a water bath (39.5 degrees C), keeping the umbilical cord moist and intact. Lambs were studied on a thermostatically controlled heating pad. Animals were prepared for either blood flow studies or micropuncture measurements. Expected differences in blood composition and cardiovascular and renal function were observed between fetuses and lambs, and values obtained for most variables were similar to those measured in chronically catheterized unanesthetized animals. Fetal GFR was much lower than that of lambs (0.20 vs. 0.62 ml.min(-1).g kidney(-1), P < 0.001). Free-flow, stop-flow, and net filtration pressures (NFP) were lower in the fetuses than the lambs (NFP 20.8 vs. 23.8 mmHg, P < 0.001), as was the calculated ultrafiltration coefficient (0.014 vs. 0.022 ml.min(-1).g(-1).mmHg(-1), P < 0.001). Thus, we conclude that rises in both net filtration pressure and the ultrafiltration coefficient contribute to the large increase in GFR between fetal life and approximately 2 wk after birth.     

A new membrane filtration medium for simultaneous detection and enumeration of Escherichia coli and total coliforms.

Recovery of total coliforms and Escherichia coli on a new membrane filtration (MF) medium was evaluated with 25 water samples from seven states. Testing of the new medium, m-ColiBlue24 broth, was conducted according to a U.S. Environmental Protection Agency protocol. For comparison, this same protocol was used to measure recovery of total coliforms and E. coli with two standard MF media, m-Endo broth and mTEC broth. E. coli recovery on the new medium was also compared to recovery on nutrient agar supplemented with 4-methylumbelliferyl-beta-D-glucuronide. Comparison of specificity, sensitivity, false positive error, undetected target error, and overall agreement indicated E. coli recovery on m-ColiBlue24 was superior to recovery on mTEC for all five parameters. Recovery of total coliforms on the new medium was comparable to recovery on m-Endo.