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WO2021046336A1 - Oligonucléotides permettant la détermination en temps réel de l'identification et de la résistance aux antibiotiques de micro-organismes pathogènes - Google Patents

Oligonucléotides permettant la détermination en temps réel de l'identification et de la résistance aux antibiotiques de micro-organismes pathogènes Download PDF

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Publication number
WO2021046336A1
WO2021046336A1 PCT/US2020/049384 US2020049384W WO2021046336A1 WO 2021046336 A1 WO2021046336 A1 WO 2021046336A1 US 2020049384 W US2020049384 W US 2020049384W WO 2021046336 A1 WO2021046336 A1 WO 2021046336A1
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WIPO (PCT)
Prior art keywords
seq
lysate
fluorophore
detecting
biological sample
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PCT/US2020/049384
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English (en)
Inventor
Robert Ulrich
Victoria E. WAGNER
Lauren MCDANIEL
John Paul
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Teleflex Medical Inc
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Teleflex Medical Inc
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Publication of WO2021046336A1 publication Critical patent/WO2021046336A1/fr
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria

Definitions

  • This invention relates generally to identification of pathogenic microorganisms. More particularly, the present invention relates, for example, to a real-time identification of a pathogenic microorganism and/or its antibiotic resistance in a biological sample via nucleic acid sequence-based amplification (NASBA) of a specific RNA sequence.
  • NASBA nucleic acid sequence-based amplification
  • BSIs Bloodstream infections
  • BSIs Bloodstream infections
  • bacteremia is a BSI that occurs when various species of bacteria enter the bloodstream. In people at risk, bacteremia may result when a person's own colonizing flora, present within their digestive tract flora, enter the bloodstream.
  • Bacteremia can be associated with an inflammatory response in the body (e.g., sepsis and septic shock).
  • sepsis and septic shock have a relatively high mortality rate.
  • Bacteria in the bloodstream can sometimes spread to other parts of the body.
  • bacteremia The symptoms of bacteremia are typically not specific, and patients will most frequently present with a fever of unknown origin. Differential diagnosis of bacteremia and sepsis can be complicated by the fact that other conditions (e.g., systemic inflammatory response syndrome (SIRS)) can present with similar symptoms.
  • SIRS systemic inflammatory response syndrome
  • Bacteremia is usually diagnosed by a combination of blood culture and post-culture testing, which also identifies the specific species. These procedures require multiple days and, in some cases, species identification can require longer than six days.
  • early initiation of appropriate therapy is important for effective treatment. For example, inadequate initial antimicrobial therapy (e.g., therapy that begins too late and/or that involves administration of an inappropriate drug) is an independent predictor of mortality, and delayed therapy is also associated with an extended length of hospital stay.
  • An aspect of the disclosure pertains to a method for detecting the presence of Staphylococcus aureus in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence- based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 1; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 2; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 3; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Staphylococcus aureus is present in the biological sample in response to
  • Another aspect of the disclosure relates to a method for detecting the presence of Escherichia coli in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 5; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 6; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 7; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Escherichia coli is present in the biological sample in response to detecting the fluorescence
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Candida albicans in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence- based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 9; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 10; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 11; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Candida albicans is present in the biological sample in response to detecting the fluorescence of the
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of a mecA gene in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence- based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 13; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 14; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 15; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the mecA gene is present in the biological sample in response to detecting the fluorescence of the
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of a cdr-1 gene in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence- based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 17; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 18; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 19; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the cdr-1 gene is present in the biological sample in response to detecting the fluor
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of a KPC gene in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence- based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 21; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 22; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 23; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the KPC gene is present in the biological sample in response to detecting the fluorescence of the fluor
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Acinetobacter baumannii in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 25; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 26; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 27; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Acinetobacter baumannii is present in the biological sample in response to detecting the
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Enterococcus faecalis in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 29; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 30; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 31; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Enterococcus faecalis is present in the biological sample
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Enterococcus faecium in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 33; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 34; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 35; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Enterococcus faecium is present in the biological sample
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Klebsiella pneumoniae in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 37; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 38; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 39; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Klebsiella pneumoniae is present in the biological sample in response to detecting the fluor
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Pseudomonas aeruginosa in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 41; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 42; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 43; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Pseudomonas aeruginosa
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Staphylococcus epidermidis in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 45; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 46; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 47; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Staphylococcus epidermidis is present in the biological sample in response
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of a OXA-48 gene in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence- based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 49; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 50; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 51; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the OXA-48 gene is present in the biological sample in response to detecting the fluor
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of a vanA gene in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence- based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 53; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 54; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 55; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the vanA gene is present in the biological sample in response to detecting the fluorescence of the fluor
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of a vanB gene in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence- based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 57; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 58; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 59; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the vanB gene is present in the biological sample in response to detecting the fluorescence of
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Candida parapsilosis in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 61; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 62; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 63; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Candida parapsilosis is present in the biological sample in response to detecting
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Streptococcus pneumoniae in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 65; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 66; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 67; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Streptococcus pneumoniae is present in the biological sample in response to
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Enterbactor cloacae complex in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 69; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 70; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 71; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Enterbactor cloacae complex is present in the biological sample
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of a NDM-1 gene in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence- based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 73; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 74; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 75; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the NDM-1 gene is present in the biological sample in response to detecting the fluorescence
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of a VIM gene in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence- based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 77; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 78; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 79; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the VIM gene is present in the biological sample in response to detecting the fluorescence of
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of a IMP-1 gene in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence- based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 81; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 82; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 83; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the IMP-1 gene is present in the biological sample in response to detecting the fluor
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Haemophilus influenzae in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 85; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 86; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 87; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Haemophilus influenzae is present in the biological sample in response to detecting the
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Neisseria meningitidis in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 89; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 90; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 91; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Neisseria meningitidis is present in the biological sample
  • Yet another aspect of the disclosure pertains to a method for detecting the presence of Enterobacter aerogenes in a biological sample.
  • the method including: lysing the biological sample to form a lysate; generating an amplified lysate by performing a nucleic acid sequence-based (NASBA) amplification for a target nucleic acid sequence in the lysate in the presence of: a forward primer including the oligonucleotide sequence of SEQ ID NO: 93; a reverse primer including the oligonucleotide sequence of SEQ ID NO: 94; and a molecular beacon including a fluorophore and the oligonucleotide sequence of SEQ ID NO: 95; exposing the amplified lysate to an excitation source; detecting a fluorescence of the fluorophore in the amplified lysate exposed to the excitation source; and determining whether the Enterobacter aerogenes is present in the biological sample in response to detecting the
  • the infection detection system including: a sampling device configured to contain a whole blood sample containing a pathogen target sequence; a lysing chamber configured to be in fluid communication with the sampling device to receive the whole blood sample, the lysing chamber being configured to lyse the whole blood sample into a lysate; a filter configured to be in fluid communication with the lysing chamber and to filter the lysate into a filter lysate; a meter configured to be in fluid communication with the filter and configured to meter a predetermined amount of filtered lysate from the filtered lysate; a NASBA fluidic network configured to be in fluid communication with the meter to receive the predetermined amount of filtered lysate, the NASBA fluidic network having: an enzyme and a primer for amplifying a predetermined genetic sequence in the pathogen target sequence contained within the predetermined amount of filtered lysate, the primer including the oligonucleotide
  • FIG. 1 illustrates a schematic infection detection system in accordance with aspects of the invention.
  • FIG. 1 shows an schematic representation of an exemplary infection detection system 10 in accordance with aspects of the invention.
  • the infection detection system is configured to process a sample and to determine whether the sample contains one or more predetermined pathogens.
  • the infection detection system in accordance with embodiments of the invention includes a sampling device 20, a lysing chamber 30, a filter 40, a meter 50, a nucleic acid sequence-based (NASBA) fluidic network 60, and an instrument 70.
  • the infection detection system also includes a sample processor 80, such as a cartridge, which at least includes the NASBA fluidic network and may include any or all of the lysing chamber, the filter, and the meter.
  • the sample processor is configured to connect to the sampling device and to receive and process a sample contained within the sampling device.
  • the sample processor may be disposable and replaceable, and may be adapted to process the collected sample using at least one NASBA assay.
  • the infection detection system may process the sample and determine whether the sample contains one or more predetermined pathogens rapidly, for example within an hour, thirty minutes, or less.
  • the infection detection system may process the sample and determine whether the sample contains one more predetermined pathogens at the point-of-care, for example within the same building, room, etc. as the patient.
  • the infection detection system thus eliminates the need for time-wasting intermediary treatment, storage, and/or extraneous transport of the sampling device.
  • the entirety of the sample processing may occur within the various components of the infection detection system thereby obviating the need of direct user intervention with the sample after the sample is collected.
  • the infection detection system may accordingly be used by a user of low skill and may be readily transported to and applied in a variety of environments (e.g., the home, a hospital room, etc.). As a result, infection in a patient may be rapidly detected and identified, which may improve the prognosis of the patient.
  • the sampling device of the infection detection system may be adapted to collect a sample, such as blood (e.g., whole blood), urine, fecal matter, purulence/pus, etc.
  • Whole blood as used herein, means blood drawn directly from a patient from which none of the components, such as plasma, platelets, or pathogens, has been removed.
  • the sampling device may collect the sample from a medical device (not shown).
  • the sampling device may be exposed for a predetermined and/or extended period of time to an internal space or lumen in the medical device so as to collect a sample of any pathogen which may form in said space and/or lumen.
  • the medical device may be an external communicating device used for treating a patient, such as a Foley catheter, a vascular catheter, a suction catheter, a bronchial scope, a urinary drain line, a respiratory suction catheter, a Bronco- Alveolar-Lavage Catheter, etc.
  • the sampling device may additionally or alternatively be adapted to collect a sample directly from a sample source such as urine, fecal matter, purulence/pus, a suspected infection site (such as a surgical dressing, wound, and/or an insertion site), etc.
  • the sampling device may additionally or alternatively be adapted to collect a sample intravenously, subcutaneously, or intraosseously.
  • the sampling device may be disposable and replaceable.
  • the sampling device may include a sample collection tube.
  • the sample collection tube may be a standard blood collection vacuum tube containing a whole blood sample. Additionally or alternatively, the sampling device may be a standard syringe containing a whole blood sample.
  • the lysing chamber may be any chamber configured to receive the whole blood sample and lyse the whole blood sample into a lysate.
  • the lysing chamber may be in fluid communication with the sampling device.
  • Fluid communication as used herein, may mean that the structures in question are fluidly connected via any of a number of structures such as tubing, conduits, etc., that allow fluid to travel from one structure to another.
  • flow of the whole blood sample from the sampling device to the lysing chamber may be operatively connected to the instrument and may be controlled and/or driven by the instrument.
  • reference is made to the instrument controlling and/or driving fluid flow for example flow of the whole blood sample from the sampling device to the lysing chamber.
  • the instrument may control and/or drive fluid flow when operatively connected to a fluid pathway and via any number of known fluid control systems, which may for example include pumps, valves, conduits etc. Further, the instrument may control and/or drive fluid flow without physically contacting the fluid. Accordingly, the sample collector and/or the sample processor maybe disposed and replaced while the instrument may be used repeatedly without contaminating the samples.
  • the lysing chamber may include all of the materials for lysing the whole blood sample and pathogen cells contained therein and for extracting and purifying pathogen messenger RNA (i.e., dissolve targeted mRNA and remove inhibitors that could interfere with nucleic acid amplification).
  • the lysing chamber may include a lysing agent, such as a lyophilized Acris lysing chemistry, that is configured to lyse the whole blood sample into the lysate.
  • the lysing chamber may physically lyse the whole blood sample ultrasonically or by freezing the whole blood sample.
  • the lysing chamber may include a plurality of chambers, for example, a first chamber and a second chamber,
  • the first chamber may include a lysing chemistry, such as, the lyophilized Acris lysing chemistry.
  • the lysing chemistry contained within the first chamber may be in the form of a reagent plug(s) having dried lysis reagents.
  • the first chamber may be in fluid communication with the sampling device and may receive the whole blood sample from the sampling device.
  • the instrument may control and/or drive flow of the whole blood sample from the sampling device to the first chamber.
  • the whole blood sample may be driven from the sampling device to the first chamber via gravity, capillary flow, etc.
  • the second chamber may include a diluent and may be in fluid communication with the first chamber.
  • the diluent may be driven from the second chamber to the first chamber to form the lysate.
  • the instrument may control and/or drive the flow of the diluent from the second chamber to the first chamber.
  • the lysate formed in the first chamber may contain the lysing agent, the diluent, and the whole blood sample.
  • the diluent may be driven to the first chamber in advance of the arrival of the whole blood sample to prepare the lysate.
  • the diluent and the whole blood sample may be driven to the first chamber simultaneously.
  • the filter is in fluid communication with the lysing chamber and is configured to filter the lysate into a filtered lysate.
  • the filter may filter out large, opaque structures from the lysate (e.g., hemoglobin) while allowing a target sequence (e.g., genetic material from target pathogens) within the lysate to pass through the filter for subsequent processing and analysis.
  • the instrument may control and/or drive the flow of the lysate from the lysing chamber and to through the filter to form the filtered lysate.
  • the meter is in fluid communication with the filter and is configured to meter a predetermined amount of filtered lysate for the NASBA analysis.
  • the predetermined amount may, for example, be between 1 and 3 ml.
  • the instrument may control and/or drive the flow of the filtered lysate from the filter and to the meter to collect the predetermined amount of filtered lysate.
  • the NASBA fluidic network may be in fluid communication with the meter and may receive the predetermined amount of filtered lysate from the meter.
  • the NASBA fluidic network may include all of the materials (e.g., reagents, structures, etc.) necessary to perform predetermined NASBA-based nucleic-acid assays for mRNA and/or DNA on the predetermined amount of filtered lysate.
  • the NASBA fluidic network may include a plurality of reaction tubes that are each directly or indirectly in fluidic communication with the meter and that are configured to receive filtered lysate from the meter.
  • the instrument may control and/or drive flow of the filtered lysate from the meter to each of the plurality of reaction tubes.
  • Each of the plurality of reaction tubes may include all of the materials for processing the filtered lysate for isothermal amplification of predetermined pathogen target sequence (e.g., targeted mRNA to identify the presence of specific genes).
  • predetermined pathogen target sequence e.g., targeted mRNA to identify the presence of specific genes.
  • Specific examples of materials that may be included in each of the plurality of reaction tubes include lysing buffers, mRNA-dependent DNA polymerase, mRNA primers, DNA primers, amino acids, and the like.
  • Each of the plurality of reaction tubes may at least include an enzyme, a primer, and a beacon for performing an NASBA assay on a pathogen target sequence within the filtered lysate.
  • Each of the plurality of reaction tubes may include one or more of the following three enzymes: Avian Myeloblastosis Virus (AMY) Reverse Transcriptase, a Ribonuclease H (RNase H), and a T7 RNA polymerase.
  • Each of the plurality of reaction tubes may include two or more oligonucleotide primers.
  • the enzyme(s) and the primer(s) may amplify a predetermined genetic sequence in the predetermined pathogen target sequence.
  • the beacon provided in each of the plurality of reaction tubes may be configured to attach to the predetermined pathogen target sequence.
  • the beacon may include a fluorophore that emits light when attached to the predetermined genetic sequence and when excited by an excitation source (e.g., a laser).
  • Each reaction tube may include at least one window such that the instrument may detect light emitted from the beacon when attached to a predetermined pathogen target sequence.
  • Each reaction tube may be provided with a beacon that is different from the beacons provided in each of the other reaction tubes. Accordingly, the NASBA fluidic network may detect as many different predetermined pathogen target sequences as there are reaction tubes.
  • the NASBA fluidic network may include a chamber containing an NASBA diluent.
  • the chamber may be in fluid communication with each of the plurality of reaction tubes.
  • the instrument may control and/or drive flow of the diluent from the chamber to each of the plurality of reaction tubes.
  • the diluent contained within the chamber may be fluidly communicated to each of the plurality of reaction tubes a predetermined period (e.g., 5 minutes) before introduction of the filtered lysate. After expiration of the predetermined period, the filtered lysate may be distributed to each of the plurality of reaction tubes to induce the NASBA reactions and the results of the NASBA reactions may be analyzed by the instrument.
  • the instrument of the infection detection system may be adapted to receive the sample processor, to initiate and/or control aspects of processing of the sample within the sample processor, and to analyze the processed sample.
  • the instrument may control and/or drive fluid flow (e.g., whole blood flow, diluent flow, lysate flow, filtered lysate flow, etc.).
  • the instrument may include a heater and/or a heat exchanger that may maintain the sample processor within a predetermined temperature range necessary for isothermal amplification of predetermined pathogen target sequences during the NASBA assays.
  • the predetermined temperature range may be within 35-50 degrees Celsius. In embodiments, the predetermined temperature range may be within 40 - 42 degrees Celsius.
  • the instrument may be configured to perform any suitable NASBA-based nucleic-acid assay on the sample utilizing the reagents.
  • the instrument may be configured to perform any steps for lysing pathogen cells and extracting and purifying pathogen messenger RNA (i.e., dissolve targeted mRNA and remove inhibitors that could interfere with nucleic acid amplification).
  • the instrument may be configured to perform any steps for processing the output solution from the extraction and purification steps for isothermal amplification of targeted mRNA to identify the presence of specific genes.
  • a biological sample includes whole blood, serum, plasma, cerebrospinal fluid (CSF), urine, synovial fluid, breast milk, sweat, tears, saliva, semen, feces, vaginal fluid or tissue, sputum, nasopharyngeal aspirate or swab, lacrimal fluid, mucous, or epithelial swab (buccal swab), and tissues (e.g., tissue homogenates), organs, bones, teeth, among others).
  • CSF cerebrospinal fluid
  • urine synovial fluid
  • breast milk sweat
  • tears saliva
  • semen semen
  • feces vaginal fluid or tissue
  • sputum nasopharyngeal aspirate or swab
  • lacrimal fluid e.g., mucous, or epithelial swab (buccal swab)
  • tissues e.g., tissue homogenates
  • a pathogenic microorganism includes, for example, one or more of Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus epidermidis, Candida parapsilosis, Streptococcus pneumoniae, Enterobacter cloacae complex, Haemophilus influenzae, Neisseria meningitidis, and Enterobacter aerogenes.
  • an antibiotic resistance includes, for example, resistance to one or more of Fluconazole, Methicillin, Carbapenem, and Vancomycin. More particularly, the pathogenic organisms and/or antibiotic resistance markers may include those listed in Table I. More particularly still, the target sequences of the pathogenic organisms and/or antibiotic resistance genes may be detected using the various forward primers, reverse primers, and molecular beacons listed in Table I (which sets forth and defines SEQ. ID. Numbers 1 through 96).
  • the forward primers, reverse primers, and molecular beacons listed in Table I are particularly suitable for use in the infection detection system 10.
  • these forward primers, reverse primers, and molecular beacons are optimized for use with a NASBA amplification and detection system.

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Abstract

L'invention concerne une méthode de détection de la présence d'organismes pathogènes et/ou de gènes de résistance aux antibiotiques dans un échantillon biologique, l'échantillon biologique étant lysé afin de former un lysat et un lysat amplifié étant généré par la réalisation d'une amplification à base de séquence d'acide nucléique (NASBA) pour une séquence d'acide nucléique cible dans le lysat. L'amplification NASBA est réalisée en présence : d'une amorce sens ; d'une amorce antisens ; et d'une balise moléculaire comprenant un fluorophore. Le lysat amplifié est exposé à une source d'excitation et une fluorescence du fluorophore est détectée dans le lysat amplifié exposé à la source d'excitation. Une présence ou non des organismes pathogènes et/ou des gènes de résistance aux antibiotiques est déterminée dans l'échantillon biologique en réponse à la détection de la fluorescence du fluorophore.
PCT/US2020/049384 2019-09-06 2020-09-04 Oligonucléotides permettant la détermination en temps réel de l'identification et de la résistance aux antibiotiques de micro-organismes pathogènes Ceased WO2021046336A1 (fr)

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Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007044873A2 (fr) * 2005-10-11 2007-04-19 Geneohm Sciences, Inc. Sequences utilisees pour la detection et l'identification de staphylococcus aureus resistant a la methiciline (sarm) des types mrej xi a xx
US20070292941A1 (en) * 2006-03-24 2007-12-20 Handylab, Inc. Integrated system for processing microfluidic samples, and method of using the same
US20090105082A1 (en) * 2006-03-24 2009-04-23 Alexander Borisovich Chetverin Non-invasive molecular colony methods, kits and apparatus
US20100075298A1 (en) * 2008-09-23 2010-03-25 The Regents Of The University Of California Method for rapid identification and quantification of microorganisms
WO2010151764A1 (fr) * 2009-06-27 2010-12-29 Pilots Point Llc Procédé et réactifs pour détecter la présence ou l'absence de staphylococcus aureus dans un échantillon de test
CN109321669A (zh) * 2018-10-29 2019-02-12 江南大学 一种基于嵌合体序列设计和分子信标的荧光检测金黄色葡萄球菌的方法

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007044873A2 (fr) * 2005-10-11 2007-04-19 Geneohm Sciences, Inc. Sequences utilisees pour la detection et l'identification de staphylococcus aureus resistant a la methiciline (sarm) des types mrej xi a xx
US20070292941A1 (en) * 2006-03-24 2007-12-20 Handylab, Inc. Integrated system for processing microfluidic samples, and method of using the same
US20090105082A1 (en) * 2006-03-24 2009-04-23 Alexander Borisovich Chetverin Non-invasive molecular colony methods, kits and apparatus
US20100075298A1 (en) * 2008-09-23 2010-03-25 The Regents Of The University Of California Method for rapid identification and quantification of microorganisms
WO2010151764A1 (fr) * 2009-06-27 2010-12-29 Pilots Point Llc Procédé et réactifs pour détecter la présence ou l'absence de staphylococcus aureus dans un échantillon de test
CN109321669A (zh) * 2018-10-29 2019-02-12 江南大学 一种基于嵌合体序列设计和分子信标的荧光检测金黄色葡萄球菌的方法

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