Patent Application
20090326211
The invention pertains to a process for concentrating fluid samples to obtain biological nucleic acid target materials for analysis.
Detection and control of microorganisms are important in many fields including health care, environmental regulation, bio-warfare, pathogen identification, food and drug testing, and in a variety of industrial systems. In industry, presence of undesirable microorganisms decreases the efficiency of operating equipment and ultimately increases the cost of associated goods or services. Furthermore, since microorganisms multiply rapidly, presence of microbial activity also causes health risks to the public. There is an increasing concern with pathogenic organisms infecting water and process system and creating increased human, animal, and environmental health risk.
In cooling towers, for example, water borne pathogenic microorganisms such as Legionella sp. may be present. If not properly treated with preferred biocides, aerosolized particles containing the microorganisms can create extreme health concerns from inhalation of the aerosolized microorganisms leading to disease such as Pontiac fever or the sometimes fatal Legionnaire's disease caused by Legionella pneumophila. Detection of this microorganism is difficult in the case of open recirculation water systems such as cooling towers because low concentrations represent serious health risk, and large water volumes must be concentrated into smaller sample volumes in order to perform the desired analytical test and obtain accurate and reproducible results.
The invention pertains to a method of treating a liquid sample having non-target microbiological particles, inorganic particles, and microbiological target species such as cells or viruses therein. The microbiological target species comprise target materials enveloped therein. The sample is passed through a prefilter medium to allow the target species to pass there through as filtrate. Some of the non-target biological particles and inorganic particles are retained on the prefilter medium. The filtrate from the prefiltering step is contacted by a main filtration medium that is adapted to retain the biological target species thereon as retentate along with other non-target microorganisms. The retentate from the main filtration step is lysed to form a lysate containing the target material.
In another aspect, the cell lysate passes through the main filtration medium and is further contacted by a post filtration medium to retain unlysed cells thereon while allowing passage of the target material therethrough as filtrate.
If desired, the main filtration medium may be pretreated with a retention enhancement agent or agents to improve the retainment of the microbiological target species on the main filter medium. In this case, the main filtration medium may be treated with a member or members chosen from the group consisting of surfactants, chelate reagents, salts, and organic solvents. These treatment agents both maintain the integrity of the microbiological target species therein (e.g., cells and viruses) during the main filter capture step and prevent the microbiological target species from irreversibly adhering to the filter material. This assures that a representative sample can be lysed and produce a testing sample that accurately represents the starting material.
In one aspect, the present invention relates to a sample collection and processing method including filtration and lysis steps. In one exemplary embodiment, the method features membranes to filter high volumes of liquid quickly and collect target components in a liquid by a two-step method including a prefiltration step and a main filtration step. The process deploys a post-concentration mechanical or non-mechanical means to release the desired enveloped target material into the solution. The sample solution is then stabilized for downstream analysis. As used herein, microbiological target species may comprise cellular organisms such as bacteria, algae, fungi, prokaryotes, etc. or viruses. As is well known, in cellular material, the target material, nucleic acid such as DNA or RNA, is located inside the cell. In a virus, the nucleic acid is located with a protein coat. “Lysing”, as used herein, is then a rupturing of the cells or protein coat to release the desired target nucleic acid material.
The method, for example, may be used to measure microbiological content. Exemplary microorganisms such as bacteria, virus, algae, fungi, and prokaryotes may be measured in accordance with the method. The biological content to be processed in accordance with the methods may be derived from any water or process system such as process water, drinking water, municipal water, cooling water, personal care product manufacturing, in-process pharmaceutical, or food and beverage processes.
In one exemplary embodiment, membranes are employed in a prefiltration system to remove any inorganic particles and large biological particles. The prefiltration membrane or membranes do not retain the target species. This membrane can be any membrane of a variety of a variety of different materials and pore sizes, but preferably one with a controlled pore size that separates at a fixed dimension. Non-limiting examples of prefiltration membrane materials are nylon, stainless steel, cellulose esters, PTFE, glass fibers, polypropylene, polyvinylchloride, hydrophilic acrylic copolymers, polyether sulfones, polycarbonates, and polyesters. Membranes of different pore sizes can be applied depending on the desired end use application. Non-limiting examples of membrane pore size for the prefiltration system are from about 1 μm, to about 100 μm, more preferably from about 1 μm to about 50 μm, but any membrane that can be used as a prefilter using the instant methods should perform a similar function and should have a well-defined pore size, e.g., a mesh structure to assure that the loss of the target materials on the prefilter membrane is minimized.
In another aspect, plural prefiltration membranes can be provided and are arranged in an upstream to downstream flow orientation. The upstream membrane or membranes will have a higher porosity than the downstream membranes.
Although we do not desire to be held to any particular theory of operation or function, it appears that the prefilter serves two purposes. First, it captures larger particles, fungi, algae, and biofilm that, if allowed to transfer to the main membrane, could agglomerate with organics and small particles and inhibit flow. This results in either long filtration times or the inability to filter the total volume required to create a representative sample. Second, the prefilter traps larger life forms like amoeba that are known to harbor Legionella. In one embodiment, the test is for planktonic Legionella, and the amoeba would expel very large numbers of Legionella if lysed.
In one exemplary embodiment wherein Legionella pneumophila is the desired microbiological target species, a pair of nylon prefiltration membranes may be used with the upstream membrane in the pair having a pore size of about 20 μm with the downstream membrane having pores on the order of about 10-11 μm.
The main filtration medium comprises a membrane designed to retain the desired target species. This species may comprise cellular materials or viruses. This membrane can be any member of a different material or pore size. Nonlimiting examples of membranes that may be used as the main filtration medium are nylon, stainless steel, cellulose esters, PTFE, glass fiber, polypropylene, polyvinyl chloride, hydrophilic acrylic copolymer, polyethersulfone, polycarbonate, and polyester. The main filtration membrane functions to retain the target component thereon as retentate. At the same time, in another aspect of the invention, after the microbiological target species containing the target material therein are lysed, the lysate may be capable of passing through the main filtration medium for subsequent downstream assay or other process.
In one aspect of the invention, the lysate may be prevented from passing through the main membrane by placing a barrier on the bottom of the membrane. The lysing action may be performed by shaking, and the lysed product may be extracted through a post concentration membrane (e.g., PES 0.2 μm).
In those instances wherein the lysate is capable of passing through the main membrane, in one embodiment, the lysate could be recirculated in a closed system on multiple passes through the main filter for a predetermined recycling time. Then, the lysate continuing the target material nucleic acid could be removed from the recirculation system for subsequent analysis.
In one embodiment wherein Legionella pneumophila is the desired biological target material, glass fiber main filtration members may be used and those having pore sizes of between about 10 μm to about 3.0 μm may be mentioned as exemplary. More preferred are those main filter membranes having pore sizes on the order of between about 0.7 μm to about 2.7 μm.
The main membrane pore size requires consideration of two characteristics. First, it must retain the desired target species thereon while not allowing them to stick to the membrane and be lysed to release the enveloped target material during the concentration step. In that case, the target materials such as nucleic acids would be released during the concentration step and be passed with the filtrate. It is desired to keep the target species (e.g., cellular and viral) intact during the concentration step so that they can be lysed during the lysing step. Second, the membrane should have sufficient porosity to assure that a large volume of sample can be filtered in a time that is practical for efficient sample testing.
The main filter membrane, in accordance with one aspect of the invention, may be treated with chemical or fluidic retention enhancement agents such as surfactants, acids, bases, chelating reagents, salts, organic solvents, etc., to enhance target species retention on the main filtration medium while allowing practical sample flow through the membrane. Suitable surfactants include zwitterionic surfactants, anionic surfactants, cationic surfactants, and nonionic surfactants.
The filtration system including both the prefiltration and main filtration media can, in one embodiment, filter quantitative broad volumes of liquid samples with high flow rates. For example, an exemplary sample volume could be 10 liters or more. The sample could be filtered by an integral filtration system with gravity or pressure assistance. Filtration by pressure includes negative pressure and positive pressure. As is conventional in the art, pumps could be used to make negative pressure such as vacuum air pumps, diaphragm liquid pumps, peristatic pumps, etc.
The target species, such as microbiological contents retained by the main filtration medium, could be used for different applications like physical, chemical, and biological characterization, etc. In processing biological contents, the main membrane containing the desired target cells is exposed to a lysing buffer designed to produce a small volume of stabilized lysate containing nucleic acid and proteins, etc. for downstream detection such as Polymerase Chain Reaction (PCR), real time PCR, reverse transcription realtime PCR, etc. or other molecular test methods. Good integrity of the nucleic acid released from the target species can be obtained if the appropriate lysing material is used and can be stabilized in the lysate for 72 hours or more at temperatures of from about 4° C.-43° C.
Target species lysing occurs by cell or protein envelope rupture and can be classified as including non-mechanical or mechanical methods. Non-mechanical methods include chemical methods, thermal methods, enzymatic methods, etc. Mechanical methods include ultrasonic disruption using a homogenizer; pressing using, for example, a French press, etc., decompression, pulverization, etc.
For non-mechanical methods, a non-limiting example is a chemical lysis method that would include any suitable chemical that can disrupt cell or protein envelope barriers. Detergents are a non-limiting example of chemicals that are commonly used to disrupt a lipid double layer membrane to release cell contents and lyse membrane protein, and non-limiting examples of suitable lysing chemicals are lithium dodecyl sulfate, CHAPS, Tween-20E, NP40, CTAB, PVPP, Triton X series detergents, sodium cholate, and sodium deoxycholate, guanidinium hydrochloride, or caustic. Chaotropic agents like guanidiunium salts can also act as lysing agents in this system. The lysing efficiency of detergents and alternate lysing agents is dependent on the cell types and specific applications. Enzymes such as lysozymes, mutanolysin, labiase, lysostaphin, lyticase, proteinase K, endolysin and achromopeptidases may be included as lysing reagents or additives to enhance lysing. Organic solvents, such as DMSO, DMF could be also included as lysing reagents or additives to enhance lysing. A host of bioscience suppliers offer a wide collection of lysing buffers suitable for cell lysis application. A variety of physical methods such as shaking, heating, cutting and homogenizing, etc., could be employed in the process to enhance the lysing efficiency. Indeed in one embodiment a cutting action may be employed in which the cells may be ruptured and the main membrane itself will be cut. Based on the complexity of the application and the nature of the target species types, single or combinations of chemical lysis methods could be used in combination with mechanical methods.
To remove the interference from undesirable cell lysates and non-lysed cells, an additional membrane or membranes could be added to process the cell lysate for downstream application. The membrane could be any membrane of different materials whose pore size is in the range of 0.22 μm to 0.45 μm for bacterial, yeast, fungi, or protogen sampling. (Virus sampling will require smaller pore sizes). Non-limited examples of these “post” filtrations membrane materials are PVDF, PES, polycarbonate, nylon, etc. This membrane acts primarily to remove large materials and/or unlysed cells from the sample to enhance long term stability of the lysate at the conditions noted above.
Although the current description emphasizes a sample concentration and process method, it is clear that the methods could be applied to laboratory, field applications, on-line, automated batch, or off-line monitoring systems as well. This expansion of capabilities allows the system to be applied to both water and in-process monitoring, as well as final process or product monitoring. Additionally, this method should be readily adapted to process flows that are known to be susceptible to microbiological growth and is not limited to water systems. Processing food, beverage, and personal care products and other systems are within the scope of this invention.
The invention will be further described in the following examples which are to be regarded as being illustrative of the invention and should not be used to limit the claims.
A variety of different membrane types were tested as prefilter or filter media so as to ensure that they were capable of filtering a 500 ml cooling water sample within a 10-minute time period. Tested, acceptable materials were found as follows.
The performance of a filtration system integrating a combination of Nylon 20 μm and Nylon 11 μm as the prefiltration membranes and a glass fiber 2.7 μm main filtration membrane was assessed to see if it could effectively provide filtration of a 500 ml cooling water sample within 10 minutes. The following results that were obtained indicate the percentage of filtrations passing the criteria versus total test runs. As can be seen in the results, the cooling water tested was taken from Chinese geographic locations and European locations.
The performance of filtration system integrating Nylon 20 μm, Nylon 11 μm as prefiltration membrane and glass fiber 2.7 μm as main membrane.
Candidate pre-filtration membranes were tested to ascertain their efficacy in allowing passage of the target material, Legionella pneumophila therethrough. Results are shown in terms of percentage of the desired target retained on the prefilter candidates.
Main membrane candidates were screened to ascertain their effectiveness in retaining the desired target material, Legionella pneumophila thereon. RNA assay of the target remaining on the main filters was made.
Main membranes screening for high cell retention elucidated by natural log of RNA copies in cells.
Main membranes were assessed for cell detention after 5 minutes of contact with a lysing buffer system at the prescribed shaking rate noted above. RNA assay of retained cells was made in order to determine the percent yield.
A series of tests were undertaken to assess lysis solution contact time with the target material and shaking time of the main membrane and retained target. Yield percent was measured by RNA assay of the target material.
Optimal shaking speeds and lysis time were determined. Based on this data, an optimal shaking speed was determined at 2× or at 100 R.P.M. with a total lysis solution contact time of 5 minutes appearing optimal.
The performance of membranes treated with a lysis buffering solution for 5 minutes was assessed. RNA assay was made to determine the amount of Legionella pneumophila in the lysate.
The performance of treated membrane with the optimized lysis buffer testing high concentrations of Legionella pneumophila (˜10̂4 CFU/assay) cells.
Selected main filter membrane and lysis buffer performance were assessed at different concentrations of the target, Legionella pneumophila cells. No treatment indicates a lack of pretreatment of the filter. STM treatment indicates that the filter was pretreated with the lysis buffering solution.
The repeatability performance of the selected membrane and lysis buffer testing different concentrations of Legionella pneumophila cells.
The repeatability of a device integrating the selected membrane and lysis buffer tested 5 log levels of Legionella pneumophila cells.
Testing was undertaken to determine the effect of an additional filtering step, after the main filtering. After prefiltering and main filtering with lysing, the lysate was passed through a PES 0.22 μm filter to retain unlysed cells and pass lysate as filtrate.
In certain exemplary aspects of the invention, the processes herein described takes less than 15 minutes from the time in which the sample collection is taken to obtain a stabilized biomaterial sample ready for transport to downstream testing. In other exemplary embodiments, stable extracts from the biomaterials are provided that retain stability for up to 72 hours at temperatures up to about 43° C.
In one exemplary embodiment, the prefiltration and main filtration steps are dead end filtering steps. Further, in varying embodiments, pretreatment of the main filter medium via surfactants or other retention enhancement agents may be employed. Surfactants may be present in concentration ranges of about 0.5% to about 5%. Further, when chelating reagents are utilized to pretreat the main filter membrane, these may be present in concentration of about 0.1 mM to 100 mM. These chelating reagents may comprise for example EDTA and EGTA etc. In further exemplary embodiments, salts may be used to pretreat the main filtration membrane, and these may be present in an amount of about 1-8 mM solutions, and in those cases in which organic solvents may be utilized for pretreatment of the main filtration medium, these may be present in an amount of about 1-10%.
Further, in order to improve lysing, the samples may be incubated at temperatures of about 30° C. to 100° C. Also, electrical fields may be employed to help release the intracellular material. Shaking, inverting, or vibration via impellers and the like may be utilized again as an aid or aids in the lysing operations. Shaking speeds of from about 10-350 RPM may be employed in those instances in which shaking may be found useful to enhance the lysing operation and the lysing operation may generally proceed for anywhere from about between 1 minute to 3 hours.
While we have shown and described herein certain embodiments of the invention, it is intended that there will be covered as well any change or modifications therein which may be made without the departing from the spirit and scope of the invention as defined in the appended claims.
