According to an aspect of the invention there is provided a method of performing one or more of: detecting, identifying and characterizing pathogens and characterizing pathogen host using markers for pathogens and hosts, comprising the steps of: a) preparing a marker-detection medium containing signatures of the identity and characteristics of pathogens and optionally of hosts; b) collecting a sample from a host; c) combining the sample with the marker-detection medium and d) analyzing the signatures to detect, identify and characterize the pathogens, and optionally, characterize the host.
DescriptionSYSTEM AND METHOD OF DETECTING PATHOGENS
Field of the Invention [00011 The present invention relates to the field of detecting pathogens. In particular, it relates to a system and method for detecting, identifying, characterizing and surveilling pathogen and host markers, collecting and disseminating information concerning those pathogens and their hosts to and from an instant location, providing treatment recommendation to and from an instant location, and providing educational information to and from an instant location.
Background of the Invention [00021 Detection and characterization of an infectious disease is a complex process that ideally begins with the identification of the causative agent (pathogen).
This has traditionally been accomplished by direct examination and culture of an appropriate clinical specimen. However, direct examination is limited by the number of organisms present and by the observer's ability to successfully recognize the pathogen.
Similarly, in vitro culture of the etiologic agent depends on selection of appropriate culture media as well as on the microbe's fastidiousness. The utility of pathogen culture is further restricted by lengthy incubation periods and limited sensitivity and specificity.
[00031 When in vitro culture remains a feasible option, the identification and differentiation of microorganisms has principally relied on microbial morphology and growth variables which, in some cases, are sufficient for strain characterization (i.e.
isoenzyme profiles, antibiotic susceptibility profiles, and chematographic analysis of fatty acids).
[00041 If culture is difficult, or specimens are not collected at the appropriate time, the detection of infection is often made retrospectively, if at all, by demonstrating a serum antibody response in the infected host. Antigen and antibody detection methods have relied on developments in direct (DFA) and indirect (IFA) immunofluorescence analysis and enzyme immunoassay (EIA)-based techniques, but these methods can also possess limited sensitivity.
[0005] These existing methods have several drawbacks. First, the process can take several days to return results. In the case of highly communicable and/or dangerous pathogens, confirmation of pathogen type may not be received until the host has already exposed others or has passed beyond treatment. Second, the transportation of samples to laboratories for culture growth increases the risk of errors, such as misidentifying the sample, or exposure of unprotected personnel to a sample containing a highly communicable pathogen. Lastly, the pathogen tests are limited based on the suspected pathogen list provided by the observer (i.e. doctor), meaning that additional unsuspected pathogens are not tested for but may be present.
100061 Related to this method of diagnosis is the response to an outbreak of infectious disease. If an outbreak is suspected or detected, the existing response is the hundreds of years old method of quarantine. One of the problems with quarantine is the delaying of correct diagnosis and treatment for individuals in quarantine.
Another is that healthy, unexposed individuals may be quarantined with infected individuals and contract a disease they would not have otherwise. Resorting to quarantine is seen as necessary due to the delays involved in detecting pathogens through blood sampling as discussed previously.
[00071 A final problem lies in identifying unknown and unsuspected pathogens.
The blood sampling tests are limited to those pathogens which are listed as suspected by the observing doctor. As many doctors may not be familiar with rare or recently identified pathogens, or may not recognize the relevant identifying symptoms, they may not list them as suspected on the sample. As a result, these pathogens remain undetected and may be unknowingly spread by the host.
[00081 In contrast to reliance on morphological characteristics, pathogen genotypic and proteomic traits generally provide reliable and quantifiable information for the detection and characterization of infectious agents. Moreover, microbial DNA/RNA can be extracted directly from clinical specimens without the need for purification or isolation of the agent.
[00091 On a global scale, molecular techniques can be applied in a high throughput manner in screening and surveillance studies monitoring disease prevalence and distribution, evaluation of control measures, and identification of outbreaks.
-2-[0010] Point-of-care diagnostic devices (PDDs) have been developed for a number of individual infectious diseases. In most cases these assays are immunochromatographic single colorimetric strip tests designed to detect a single infectious agent (either a pathogen-specific antigen or an antibody response to one) in a small volume of blood or serum.
[0011] None of these current assays has the capability to detect multiple pathogens or simultaneously detect genomes and proteomes of multiple pathogens. Similar limitations exist for other rapid diagnostic assays. Since almost all these tests rely on a single visual colorimetric change for their readout, the opportunities to detect multiple pathogens are severely impeded and the majority of current PDDs are restricted to the detection of a single pathogen. Consequently, evaluating patients for potential infectious agents or testing a unit of blood for common transmissible agents requires multiple consecutive point-of-care tests to be performed, complicating clinical management, slowing results and significantly escalating costs.
[0012] Many PDDs do not meet what are considered essential requirements including: ease of performance, a requirement for minimal training, the generation of unambiguous results, high sensitivity and specificity, the generation of same day results (preferably within minutes), relative low cost, and no requirement for refrigeration or specialized additional equipment.
[0013] In summary, despite current availability of excellent diagnostic reagents (e.g.
antibody and nucleic acid probes) that recognize specific targets for many microbial pathogens, the current strategies have inadequate performance characteristics.
Contributing to this is the fact that these reagents are conjugated to organic dyes, gold-labelled particles or enzymes that lack sufficient sensitivity to be detected at the single molecule level. Furthermore, the current PDD platforms and detection schemes typically rely on single macroscopic colorimetric changes and are not well suited to the simultaneous detection of multiple pathogens.
100141 More recent advances in molecular diagnostics, including real-time PCR
combined with automated specimen processing, have addressed a number of the limitations of earlier "in-house" and non-standardized gene amplification assays. These assays represent a significant advance in detecting, quantifying, and characterizing many
-3-microbes and currently represent the "gold" or reference standard for infectious disease diagnostics for a number of pathogens. However, these assays are still complex, expensive, and require specialized equipment, creating a number of barriers to their potential application at point-of-care.
[0015] Finally, current genomic or proteomic detection strategies require a sample processing and technical commitment to one strategy or the other. There is no current capacity to simultaneously detect both antigenic targets for some pathogens and genetic targets for others. This limits the simultaneous detection of preferred pathogen-specific targets and presents a barrier to fully exploiting the complementary power of both strategies.
[0016] A system is needed which enables pathogen detection, identification and characterization, as well as host characterization in a much more timely manner than existing methods. Preferably, such a system would also enable detection, identification and characterization of many or all pathogens in a sample based on an existing database and not be limited to a suspected list provided by a observing doctor.
Summary of the Invention [0017] According to an aspect of the invention there is provided a method of performing one or more of: detecting, identifying and characterizing pathogens and characterizing pathogen hosts using markers for pathogens and hosts, comprising the steps of: a) preparing a marker-detection medium containing signatures of the identity and characteristics of pathogens and optionally of hosts; b) collecting a sample from a host; c) combining the sample with the marker-detection medium and d) analyzing the signatures to detect, identify and characterize the pathogens, and optionally, characterize the host.
[0018] Preferably, the sample collected is a blood sample, although plasma, serum and other types of samples can also be used, and the pathogen-detection medium preferably consists of nanobeads conjugated to biorecognition molecules (BRMs) and the nanobeads are injected with quantum dots. Also preferably, each of the nanobeads contains a unique combination of quantum dots to provide a unique optical barcode
-4-associated with each nanobead for detecting unique molecular signatures of each pathogen and for characteristics of each pathogen and host.
[00191 Preferably, the analyzing step consists of illuminating the combined sample with a laser and obtaining resulting spectra with a spectrometer/CCD camera.
These spectra correlate with identified individual molecular markers of the pathogen and host.
[00201 Optionally, the method may include producing a list of host characterization markers associated with said host sample as part of analysis step d). .
[00211 Optionally, the method may include an additional step e) of providing a list of treatment options based on the list of pathogen and host markers generated in analysis step d).
100221 Optionally, the method may include step f) of providing to an instant location educational information based on the list of pathogen and host markers generated in analysis step d).
[00231 Preferably, the method further includes an additional step g) of transmitting said list of pathogen markers and said list of host identifier markers to a remote database.
[00241 According to another aspect of the invention a system of components is provided which is capable of executing any of the above methods.
[00251 The advantages of the present invention include a vast reduction in the amount of time necessary to identify pathogens in a patient sample, as well as the ability to provide immediate on-site information concerning treatment and quarantine measures for any identified pathogens. Another advantage is the ability to collect patient and pathogen data in a global database and mine the information contained in this database to produce trends and tracking measures for various pathogens and their hosts, which information may be used for surveillance, research, therapeutic design, and other purposes.
100261 Other and further advantages and features of the invention will be apparent to those skilled in the art from the following detailed description thereof, taken in conjunction with the accompanying drawings.
-5-Brief Description of the Drawings [00271 The invention will now be described in more detail, by way of example only, with reference to the accompanying drawings, in which like numbers refer to like elements, wherein:
Figure 1 is a flow chart detailing the series of steps in the inventive method disclosed herein;
Figure 2 is a block diagram for a pathogen detection device; and Figure 3 is a block diagram of multiple devices communicating with a central database.
Detailed Description of the Preferred Embodiments [00281 Referring now to Figure 1, the present inventive method is described by a series of steps set out in a flowchart.
100291 The first step 12 is to collect a sample from a host (e.g. a human, animal or environmental sample), preferably a blood sample, although plasma samples, serum samples and other types of physical samples can be used, as appropriate. This sample is then analyzed 14 and a list of pathogens contained in the sample is generated 16.
[00301 The analysis 14 is performed by a pathogen detection device 30 as shown in Figure 2. This device 30 is portable, preferably hand-held, and has an outlet 32 for receiving a sample and a display 36 to show the list of detected pathogens within the sample. An input device 38, such as a keyboard, is also provided to enable scrolling and viewing of the display and input of additional information (field notes, etc.). The list of pathogens is generated from a database of known pathogens, which may be an internal database on the device 30 (kept in flash memory or similar storage to allow for updating) or retrieved by communicating with an external database. The pathogen detection device 30 is ideally capable of detecting multiple pathogen and host markers within a single sample, and preferably markers of different types, such as protein-based markers and gene-based markers.
-6-[00311 The method of detection used can be varied among suitable available methods, however, a preferred method is the use of quantum dots bonded to biorecognition molecules (BRMs). Quantum dots, also known as semiconductor nanocrystals, are electromagnetically active nanotechnologic particles, ranging in size from 2 nanometers (nm) to 8 nm. A particularly useful property of quantum dots is that they are fluorescent, that is they emit light after brief illumination by a laser. In addition, quantum dots of different sizes will fluoresce in different colors and the fluorescing color can be modified by the particle's shape, size and composition. BRMs are biological molecules that bind only to a single other biological molecule. For example, "antibodies"
are BRMs that bind to proteins and "oligonucleotide probes" are BRMs that bind to genes (e.g. DNA or RNA). Pathogens and hosts have both unique and shared genetic and protein markers, and each marker can be bonded to by a specific BRM.
[00321 A nanobead, which is a plastic bead that can be 1-10 microns in diameter and injected with a collection of quantum dots, is physically conjugated to a BRM.
By injecting unique combinations of quantum dots into the nanobeads, thousands of nanobeads with distinctive combinations of quantum dots can be created. When a laser illuminates the nanobeads, the quantum dots fluoresce to produce a distinctive combination of colors. These color combinations are an example of a barcode, in this case an optical bar code, analogous to a UPC symbol, and similar known types of imprinted barcodes. Since each BRM recognizes a distinct pathogen or host marker and each nanobead has a unique barcode, each BRM-conjugated nanobead provides a barcode for a specific pathogen or host marker. Thousands of these BRM-conjugated nanobeads may be dried into a powder and provided in sample vials.
[0033] The biological (e.g. blood) sample is added to a vial, and the various nanobeads become attached to different pathogens based on the BRM conjugated to the nanobeads. The vial is then illuminated by a laser, causing the quantum dots to fluoresce.
The resulting spectrum is analyzed by the marker detection device and, by comparing the spectrum data with a database of known spectra corresponding to different pathogens and host characteristics, a list of detected pathogens and pathogen and host characteristics is produced. The response time from the taking of the original biological sample to the production of the pathogen list can be measured in minutes.
-7-[0034] Ideally, the pathogen detection device 30 is a portable, hand-held device with an integrated laser and spectrometer and includes a supply of sample vials.
The device 30 may store a pathogen identity database on board, or access a remote database, preferably via the Internet, preferably wirelessly, and identify the pathogen from a remote, central database. If an on-board database is used, a communications system 34 for contacting and receiving updates from a larger, central database should be provided.
[00351 Once the pathogen list is produced, the pathogen detection device 30 may additionally provide further information of value to the diagnosing doctor.
Ideally, a treatment protocol is provided (step 18), including any special measures necessary to avoid communication of the pathogen. Other information, such as pathophysiology, disease history and bibliographic references can be provided, enabling the pathogen detection device 30 to also be used as an educational tool in the appropriate scenarios.
[00361 An outbreak scenario for use of the device in a standard pathogen detection setting follows. An airport is a point of entry representing a major pathogen travel vector, as well as presenting problems with implementing traditional detection and quarantine methods. By equipping medical staff with a number of pathogen detection devices as described herein, and a supply of nanobead sample vials, incoming passengers can be processed on-site by taking a blood sample and injecting it into a sample vial. The analysis is performed by the pathogen detection device within minutes and the sampled passenger can be quickly released or redirected for treatment and observation, as necessary. While a single device is limited in processing capability, the ability to provide multiples of identical devices can enable processing of passengers in a matter of hours, not days. Faster processing allows appropriate treatment and quarantine measures to be taken earlier, and be more effective, reducing the probability of the pathogen spreading unchecked.
[00371 Detecting and providing a treatment protocol for a pathogen represents merely the first step in a potentially much larger process for tracking and controlling pathogens as shown in Figure 3. By providing a sufficient number of BRM-conjugated nanobeads, the pathogen and the human or animal host for the pathogen can be characterized by thousands of genetic and protein markers contained in a biological sample, such as blood.
This information, which does not include any other information about the patient (e.g.
-8-name, address and other privacy-protected data), but which does include GPS
locator information to identify the location of the sample, is then sent to a central database 40.
The information is preferably sent wirelessly, and immediately upon generation of the pathogen list (step 20). The central database 40 is in contact with a substantial number of pathogen detection devices 30 at any given time.
[0038] The central database 40 can be local, national or global, or a combination of different databases of these types. Ideally, one top-level central database 40 is provided which receives information constantly from all devices 30 worldwide. Over time, the database becomes a collection of information concerning every known pathogen and probable or possible mutations, the locations where outbreaks have occurred and the types of humans or animals (based on gene and protein code data) who have been exposed to certain pathogens. The information contained in this database can then be mined to detect patterns.
[0039] Some patterns developed from the collected data include outbreak tracking, by identifying geographic regions where outbreaks of specific pathogens occur regularly.
Other patterns can be developed from the human or animal host data, including susceptibility of certain segments of the population to certain pathogens, and resistance of other segments of the population to other pathogens.
[0040] This concludes the description of a presently preferred embodiment of the invention. The foregoing description has been presented for the purpose of illustration and is not intended to be exhaustive or to limit the invention to the precise form disclosed. Many modifications and variations are possible in light of the above teaching and will be apparent to those skilled in the art. It is intended the scope of the invention be limited not by this description but by the claims that follow.
-9-
Claims (18) What is claimed is:1. A method of performing one or more of: detecting pathogens, identifying pathogens, characterizing pathogens and characterizing pathogen hosts, comprising the steps of:
a) preparing a pathogen-detection medium for detection of pathogen and host markers;
b) collecting a sample from a host;
c) combining said sample with said pathogen-detection medium containing pathogen-specific detectors; and d) analyzing said combined sample to produce a list of pathogens contained within the host, and a list of pathogen and host characteristics.
2. The method of claim 1, wherein said sample collected in said collecting step b) is a one of: a blood sample, a plasma sample, and a serum sample.
3. The method of any of claims 1-2, wherein said pathogen-detection medium consists of nanobeads conjugated to biorecognition molecules (BRMs) and said nanobeads are injected with quantum dots.
4. The method of any of claims 1-3, wherein each of said nanobeads contains a unique combination of quantum dots to provide a unique optical barcode associated with said each nanobead.
5. The method of any of claims 1-4, wherein said analyzing step consists of illuminating said combined sample with a laser and measuring a resulting spectrum with a spectrometer.
6. The method of any of claims 1-5, further including an additional step e) of providing a list of treatment options based on the list of pathogens generated in analysis step d).
7. The method of any of claims 1-6. further including producing a list of host characteristic markers associated with said host sample as part of analysis step d).
8. The method of any of claims 1-7, further including an additional step f) of transmitting said list of pathogens and pathogen characteristics and said list of host characteristic markers to a remote database.
9. A system for one or more of: detecting pathogens, identifying pathogens, characterizing pathogens and characterizing pathogen hosts, comprising:
a) a sample medium containing pathogen-specific detectors to be combined with a host sample; and b) a pathogen detection device for analyzing said sample medium and generating a list of pathogens and pathogen and host characteristics detected within said sample medium.
10. The system of claim 9, further including a database containing information on different pathogens and a connection on said pathogen detection device to enable communication with said database.
11. The system of any of claims 9-10, wherein said connection to said database is provided by a wireless communications network.
12. The system of any of claims 9-11, wherein said sample medium consists of nanobeads conjugated to biorecognition molecules (BRMs) and said nanobeads are injected with quantum dots and said host sample is one of: a blood sample, a plasma sample and a serum sample.
13. The system of any of claims 9-12, wherein each of said nanobeads contains a unique combination of quantum dots to provide a unique optical barcode associated with said each nanobead.
14. The system of any of claims 9-13, wherein said pathogen detection device consists of a laser and a spectrometer for illuminating said sample and measuring a resulting spectrum.
15. The system of any of claims 9-14, wherein said pathogen detection device further provides a list of treatment options based on the list of pathogens generated.
16. The system of any of claims 9-15, wherein said pathogen detection device further generates a list of host characterization markers associated with said host sample.
17. The system of any of claims 9-16, wherein said list of host characterization markers and said list of pathogens and pathogen characteristics is uploaded to said database.
18 The system of any of claims 9-17, wherein uploading to said database occurs automatically upon generation of said lists.
CA002536698A 2006-02-15 2006-02-15 System and method of detecting, identifying and characterizing pathogensand characterizing hosts Abandoned CA2536698A1 (en) Priority Applications (15) Application Number Priority Date Filing Date Title CA002536698A CA2536698A1 (en) 2006-02-15 2006-02-15 System and method of detecting, identifying and characterizing pathogensand characterizing hosts CA002571904A CA2571904A1 (en) 2006-02-15 2006-12-19 System and method of detecting pathogens PCT/CA2007/000211 WO2007093043A1 (en) 2006-02-15 2007-02-13 Method for detecting pathogens using microbeads conjugated to biorecognition molecules MX2008010541A MX2008010541A (en) 2006-02-15 2007-02-13 Method for detecting pathogens using microbeads conjugated to biorecognition molecules. KR1020147000928A KR101518765B1 (en) 2006-02-15 2007-02-13 Method for detecting pathogens using microbeads conjugated to biorecognition molecules CA002636489A CA2636489C (en) 2006-02-15 2007-02-13 System and method of detecting pathogens BRPI0708468-4A BRPI0708468A2 (en) 2006-02-15 2007-02-13 Pathogen detection method using micro-beads conjugated with biorecognition molecules US12/279,639 US20100021937A1 (en) 2006-02-15 2007-02-13 Method for detecting pathogens using microbeads conjugated to biorecognition molecules KR1020087022364A KR101431843B1 (en) 2006-02-15 2007-02-13 Detection of pathogens using microbeads conjugated to biomolecules EP07719377A EP1994166A4 (en) 2006-02-15 2007-02-13 Method for detecting pathogens using microbeads conjugated to biorecognition molecules CN2007800056984A CN101384725B (en) 2006-02-15 2007-02-13 System and method of detecting pathogens JP2008554569A JP5114432B2 (en) 2006-02-15 2007-02-13 Pathogen detection system and method using microbeads bound to biological substance recognition molecule HK09108325.0A HK1128735B (en) 2006-02-15 2007-02-13 A system for detecting pathogens ZA2008/07871A ZA200807871B (en) 2006-02-15 2008-09-12 Method for detecting pathogens using microbeads conjugated to biorecognition molecules US15/184,519 US20160299137A1 (en) 2006-02-15 2016-06-16 Method for detecting pathogens using microbeads conjugated to biorecognition molecules Applications Claiming Priority (1) Application Number Priority Date Filing Date Title CA002536698A CA2536698A1 (en) 2006-02-15 2006-02-15 System and method of detecting, identifying and characterizing pathogensand characterizing hosts Publications (1) Publication Number Publication Date CA2536698A1 true CA2536698A1 (en) 2007-08-15 Family ID=38421222 Family Applications (1) Application Number Title Priority Date Filing Date CA002536698A Abandoned CA2536698A1 (en) 2006-02-15 2006-02-15 System and method of detecting, identifying and characterizing pathogensand characterizing hosts Country Status (2) Families Citing this family (3) * Cited by examiner, â Cited by third party Publication number Priority date Publication date Assignee Title NZ593660A (en) * 2011-06-22 2013-05-31 Zyzeba Testing Ltd Method of tracking spread of microorganisms using optical determination of microorganism populations at known locations and transmission of results of determination to a remote collection device CN103499685B (en) * 2013-10-15 2015-09-09 çè¿æ° People's urinary system cause of disease bacterium infects the preparation method of the immunofluorescence diagnostic reagent of clinical diagnosis US10935535B2 (en) * 2017-08-09 2021-03-02 Fremonta Corporation Method and apparatus for applying aggregating sampling to food items Family Cites Families (1) * Cited by examiner, â Cited by third party Publication number Priority date Publication date Assignee Title CA2450725A1 (en) * 2001-06-28 2003-01-09 Advanced Research And Technology Institute, Inc. Methods of preparing multicolor quantum dot tagged beads and conjugates thereofEffective date: 20180703
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