US20150259729A1 - Methods of detecting multi-drug resistant organisms - Google Patents

Methods of detecting multi-drug resistant organisms Download PDF

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US20150259729A1
US20150259729A1 US14/657,908 US201514657908A US2015259729A1 US 20150259729 A1 US20150259729 A1 US 20150259729A1 US 201514657908 A US201514657908 A US 201514657908A US 2015259729 A1 US2015259729 A1 US 2015259729A1
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patient
antibiotic
oxa
nucleic acid
recommending
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George Terrance Walker
Tony Rockweiler
Alex Saeed
Vadim Sapiro
Rossio Kersey
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Opgen Inc
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    • 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
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    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
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    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
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Definitions

  • the present invention relates generally to the identification and characterization of genes and gene families associated with multi-gene resistance in biological samples in the screening, diagnosis, therapy, epidemiological surveillance, and monitoring of multi-gene resistant colonization and infection.
  • Antibiotic-resistant bacterial infections are associated with poor clinical outcomes including increased morbidity, mortality, and healthcare costs among infected patients.
  • Colonized patients are an important reservoir of beta-lactamases leading to the transmission and spread of these organisms within hospitals and long term care facilities. The prevalence of these organisms in such facilities in the United States has steadily increased over the last 30 years.
  • Treatment options for patients with multi-drug resistant organisms (MDROs) are extremely limited; therefore prevention of transmission within these facilities is paramount.
  • Classical culture methods for detection of MDROs are time consuming (48-72 hours), leading to delays, inappropriate treatment and patient isolation.
  • Highly sensitive, rapid molecular methods for detection of MDROs provide a tool for surveillance and screening of high risk patients and better patient management. The present invention addresses this market need.
  • the invention is based upon an ultra-sensitive method for detecting multi-drug resistant bacterial colonization or infection in a subject.
  • the invention relates to methods for the rapid detection and characterization of MDROs, bacteria, viruses, fungi, yeasts, and molecular, phenotypic, and host biomarkers associated with infectious diseases, through high density matrix gene testing in order to provide the most comprehensive, high resolution profile of colonization, infection, and resistance pattern in a test sample.
  • the method includes isolating a nucleic acid sample from a biological sample obtained from the patient by amplifying the antibiotic resistant genes KPC, NDM, OXA, VIM, IMP, CTX-M and VanA by contacting the nucleic acid sample with one or more amplification primers that specifically hybridize with the each of the antibiotic resistant genes to provide an enriched nucleic acid sample; detecting the presence of the antibiotic gene by contacting the nucleic acid sample with one or more detection primers that specifically hybridize with the each of the antibiotic resistant genes to in the enriched nucleic acid sample; classifying the patient as having a multi-drug resistant bacterial colonization or infection when one or more of the antibiotic resistant genes are identified in the enriched nucleic acid sample; and providing a contact precautions recommendation for the patient having a multi-drug resistant bacterial colonization or infection.
  • the antibiotic resistant genes further include one or more of IMI, SME, GIM, SPM, NMC, SFC, SHV, TEM, BEL, VEB, GES, PER, SFO, BES, TLA, ACC, CMY, MIR, ACT, DHA, MOX, FOX, or CFE.
  • the method further includes making a treatment recommendation for the patient.
  • Treatment recommendation include recommending that the patient does not receive a carbapenem antibiotic when KPC, NDM, OXA, VIM, IMP, SME, SPC, IMI, NMC, or CcrA is detected; recommending that the patient does not receive a cephalosporin antibiotic when CTM-X, PER, VEB, GES, BES, SFO, TLA, TEM with amino acid substitutions E104K, R164H, R164S, R164C, G238S or E240K, or SHV with amino acid substitutions G156D, G238S or E240K, is detected recommending that the patient does not receive a beta-lactamase inhibitor-beta-lactam combination when ACC, MOX, CMY, CFE, ACT, DHA or FOX is detected; or recommending that the patient does not receive vancomycin when VanA is detected.
  • the method further includes testing the biological sample to identify the phenotype of the multi-drug resistant organism and/or culturing the biological sample and confirming drug resistance.
  • the invention includes methods of making a treatment recommendation for a subject known to or suspected of being colonized with or having a bacterial infection isolating a nucleic acid sample from a biological sample obtained from the patient by amplifying the antibiotic resistant genes KPC, NDM, OXA, VIM, IMP, CTX-M and VanA and optionally one or more of IMI, SME, GIM, SPM, NMC, SFC, SHV, TEM, BEL, VEB, GES, PER, SFO, BES, TLA, ACC, CMY, MIR, ACT, DHA, MOX, FOX, or CFE by contacting the nucleic acid sample with one or more amplification primers that specifically hybridize with the each of the antibiotic resistant genes to provide an enriched nucleic acid sample; detecting the presence of the antibiotic gene by contacting the nucleic acid sample with one or more detection primers that specifically hybridize with the each of the antibiotic resistant genes to in the enriched nucleic acid sample recommending that the patient does not
  • the invention includes methods of making a treatment recommendation for a healthy subject by isolating a nucleic acid sample from a biological sample obtained from the patient; amplifying the antibiotic resistant genes KPC, NDM, OXA, VIM, IMP, CTX-M and VanA and optionally one or more of IMI, SME, GIM, SPM, NMC, SFC, SHV, TEM, BEL, VEB, GES, PER, SFO, BES, TLA, ACC, CMY, MIR, ACT, DHA, MOX, FOX, or CFE by contacting the nucleic acid sample with one or more amplification primers that specifically hybridize with the each of the antibiotic resistant genes to provide an enriched nucleic acid sample; detecting the presence of the antibiotic gene by contacting the nucleic acid sample with one or more detection primers that specifically hybridize with the each of the antibiotic resistant genes to in the enriched nucleic acid sample and recommending that the patient does not receive a carbapenem antibiotic when K
  • the invention further includes methods of identifying the emergence of a multi-drug resistant organism in a population of subjects identifying one or more antibiotic resistant genes selected from KPC, NDM, OXA, VIM, IMP, CTX-M and VanA and optionally one or more of IMI, SME, GIM, SPM, NMC, SFC, SHV, TEM, BEL, VEB, GES, PER, SFO, BES, TLA, ACC, CMY, MIR, ACT, DHA, MOX, FOX, or CFE in a plurality of subject samples wherein identification of an antibiotic resistant genes in the plurality of subject samples indicates the emergence of a multi-drug resistant organism in a population.
  • one or more antibiotic resistant genes selected from KPC, NDM, OXA, VIM, IMP, CTX-M and VanA and optionally one or more of IMI, SME, GIM, SPM, NMC, SFC, SHV, TEM, BEL, VEB, GES, PER, S
  • the invention provides methods of screening a patient for multi-drug resistant bacterial colonization or infection by isolating a nucleic acid sample from a biological sample obtained from the patient such that the sample is substantially free of protein, cellular debris and or PCR inhibitors and identifying one or more antibiotic resistant genes selected from KPC, NDM, OXA, VIM, IMP, CTX-M and VanA and optionally one or more of IMI, SME, GIM, SPM, NMC, SFC, SHV, TEM, BEL, VEB, GES, PER, SFO, BES, TLA, ACC, CMY, MIR, ACT, DHA, MOX, FOX, or CFE in the sample wherein identification of an antibiotic resistant genes indicates the subject is colonized or infected with a multi-drug resistant bacterial organism.
  • the invention provides surveillance methods to establish source of the infection or colonization, comprising by extracting a nucleic acid sample from a sample collected from the environment; amplifying the antibiotic resistant genes KPC, NDM, OXA, VIM, IMP, CTX-M and VanA and optionally one or more of IMI, SME, GIM, SPM, NMC, SFC, SHV, TEM, BEL, VEB, GES, PER, SFO, BES, TLA, ACC, CMY, MIR, ACT, DHA, MOX, FOX, or CFE by contacting the nucleic acid sample with one or more amplification primers that specifically hybridize with the each of the antibiotic resistant genes to provide an enriched nucleic acid sample; detecting the presence of the antibiotic gene by contacting the nucleic acid sample with one or more detection primers that specifically hybridize with the each of the antibiotic resistant genes to in the enriched nucleic acid sample; wherein the presence of the antibiotic gene in the sample indicates the source of the infection or colon
  • the patient is at high risk for having a multi-drug resistant bacteria colonization or infection.
  • Contact precautions includes for example, isolating the patient to a quarantine area or ward, providing a private room for said patient, donning personal protective apparel upon entering the patient's room, limiting patient mobility, limiting or restricting access of non-colonized or non-infected patients or medical personnel to the patient, or providing dedicated patient care equipment.
  • Biological samples include but are not limited to an anal swab, a rectal swab, a skin swab, nasal swab, wound swab, stool, blood, plasma, serum, urine, sputum, respiratory lavage, cerebrospinal fluid, bacteria culture or bacteria isolate, fungal culture or fungal isolate, virus culture or virus isolate.
  • kits for determining whether a patient is colonized or infected with a multi-drug resistant bacteria including a biological sample collection means; one or more primers that specifically hybridize with one or more antibiotic resistant genes selected from KPC, NDM, OXA, VIM, IMP, CTX-M and VanA and optionally one or more of IMI, SME, GIM, SPM, NMC, SFC, SHV, TEM, BEL, VEB, GES, PER, SFO, BES, TLA, ACC, CMY, MIR, ACT, DHA, MOX, FOX, or CFE; a control sample; and an instruction, wherein the instruction classifies the patient as being colonized or infected with a multi-drug resistant bacteria when one or more of the antibiotic resistant genes are identified in the sample.
  • the invention provides method for implementation by one or more data processors forming part of at least one computing system by receiving, by at least one data processor, data characterizing test results of biological specimens for a patient or group of patients, wherein the test results characterize an outcome of a nucleic acid sample contacted with one or more primers that specifically hybridize with one or more antibiotic resistant genes selected from KPC, NDM, OXA, VIM, IMP, CTX-M and VanA and optionally one or more of IMI, SME, GIM, SPM, NMC, SFC, SHV, TEM, BEL, VEB, GES, PER, SFO, BES, TLA, ACC, CMY, MIR, ACT, DHA, MOX, FOX, or CFE; and generating, using at least one data processor and the received data, a database of test results for the patient or group of patients.
  • the method further includes aggregating the database of test results with additional individual patient health data, patient group demographic data, healthcare institution demographic data, regional, national, or global geographic healthcare data.
  • the method further includes establishing, using the database of test results, colonization or infection rates and trends.
  • the method further includes monitoring, using the database of test results, Hospital Acquired Infection (HAI) and death rates, CRE infection or death rates, ESBL infection or death rates.
  • HAI Hospital Acquired Infection
  • CRE infection or death rates CRE infection or death rates
  • ESBL infection or death rates CRE infection or death rates
  • the method further includes establishing or augmenting, using the database of test results, treatment guidelines and policies, infection control procedures, or healthcare economic and risk management policies.
  • the method further includes computing, using the database of test results, baseline MDRO infection rates for a hospital and measuring the rate against a regional or national rate.
  • the method further includes comprising augmenting treatment procedures, using the database of test results, to lower patient Length of Stay (LOS) in a healthcare institution, to lower overall costs, to lower patient death rates due to MDRO, to lower CMS penalties for HAIs, and to lower risk of legal settlements due to wrongful death claims.
  • LOS Patient Length of Stay
  • the database of test results further includes an Electronic Health Record (EHR) or Laboratory Information Management System (LIMS).
  • EHR Electronic Health Record
  • LIMS Laboratory Information Management System
  • Computer program products are also described that comprise non-transitory computer readable media storing instructions, which when executed by at least one data processors of one or more computing systems, causes at least one data processor to perform operations herein.
  • computer systems are also described that may include one or more data processors and a memory coupled to the one or more data processors.
  • the memory may temporarily or permanently store instructions that cause at least one processor to perform one or more of the operations described herein.
  • methods can be implemented by one or more data processors either within a single computing system or distributed among two or more computing system.
  • FIG. 1 is an illustration showing that the assay of the invention is capable of presumptively stratifying bacterial species based upon test results.
  • FIG. 2 is an chart showing the limits of detection (CFU/swab) of the methods of the invention
  • FIG. 3 is a chart showing the specificity of the methods of the invention.
  • FIG. 4 is a chart showing the reproducibility of the methods of the invention.
  • FIG. 5 is a summary of genes and gene families used in the Resistome Test.
  • FIG. 6 illustrates the Resistome Test used as a first-line screen for establishing resistance profiles in combination with DNA sequencing for high resolution strain typing.
  • FIG. 7 illustrates the utility of the Resistome Test used in combination with DNA sequencing data to establish gene transmission profiles and events.
  • FIG. 8 illustrates an example of using the Resistome Test for reporting and mapping individual patient anatomical and point-source environmental data.
  • FIG. 9 illustrates an example of using the Resistome Test for reporting and mapping multiple patient data across a hospital setting.
  • the present invention relates to methods for the rapid detection of multi-drug resistant organisms (MDROs).
  • MDROs multi-drug resistant organisms
  • the methods are useful in the detection of subjects that are colonized or infected with MDROs. Detection of MDRO colonized or infected subjects aid in infection control and the selection of appropriate antibiotic therapy.
  • the methods of the invention detects a broad number of genes that make up the “resistome” of organisms or the collection of antibiotic resistance in pathogeneic and non-pathogenic bacteria ( FIG. 5 ).
  • the methods of the invention detect beta-lactamase genes found in beta-lactam antibiotic resistant gram negative bacteria and vanomycin resistant genes found in vancomyocin resistant gram positive bacteria.
  • KPC Klebsiella pneumoniae carbapenemase
  • NPM New Delhi Metallo-beta-lactamase
  • VIM Verona integron-encoded metallo- ⁇ -lactamase
  • IMP IMP
  • CTX-M CTX-M gene found in extended spectrum resistant gram-negative bacteria
  • VanA found in vancomycin resistant Enterococcus
  • IMI-type carbapenemase IMI
  • the methods of the invention can further include the detection of numerous infectious disease organisms of biomarkers in combination with the MDRO-associated genes.
  • numerous infectious disease organisms of biomarkers for example, in some aspects Clostridium difficile , norovirus or Methicillin-resistant Staphylococcus aureus (MRSA) are detected.
  • MRSA Methicillin-resistant Staphylococcus aureus
  • the methods of the invention can include the detection and characterization of resistome genes and resistome gene patterns in biological samples as a first-line typing screen for subsequent higher discrimination molecular typing methods downstream for example DNA whole Genome Sequencing as part of a comprehensive solution for high resolution strain typing and mapping gene transmission events. ( FIGS. 6 and 7 )
  • KPC-2 through KPC-11 are known, and they are distinguished by one or two amino acid substitutions (KPC-1 was re-sequenced in 2008 and found to be 100% homologous to published sequences of KPC-2).
  • KPC-1 was found in North Carolina, KPC-2 in Baltimore and KPC-3 in New York. They have only 45% homology with SME and NMC/IMI enzymes and, unlike them, can be encoded by self-transmissible plasmids.
  • KPC Klebsiella pneumoniae carbapenemase
  • Chromosomal and plasmid-mediated extended-spectrum ⁇ -lactamases (carbapanemases), identified in Klebsiella pneumonia, Escherichia coli and Enterobacter spp, Serratia marcescens, Pseudomonas putida and Citrobacter freundii worldwide. Divided into 16 subtypes i.e. KPC-1 to KPC-16. Hydrolyzes ⁇ -lactams from the penicillin (i.e. ampicillin, piperacillin, benzylpenicillin, and cloxacillin), cephalosporin (i.e. cefotaxime and ceftazidime, cephaloridine), carbapenem (i.e.
  • iminipenen, meropenem, etrapenem, doripenem), and monobactam (i.e. aztreonam) groups at different rates. Hydrolyze oxyminio-cephalosporins more efficiently than other carbapenemases. Weakly Inhibited by clavuanic acid and tazobactam.
  • VIM-1 was discovered in P. aeruginosa in Italy in 1996; since then, VIM-2—now the predominant variant—was found repeatedly in Europe and the Far East; VIM-3 and -4 are minor variants of VIM-2 and -1, respectively.
  • VIM enzymes occur mostly in P. aeruginosa , also P. putida and, very rarely, Enterobacteriaceae. Forty gene subtypes have been reported for
  • Amino acid sequence diversity is up to 10% in the VIM family, 15% in the IMP family, and 70% between VIM and IMP. Enzymes of both the families, nevertheless, are similar. Both are integron-associated, sometimes within plasmids. Both hydrolyse all ⁇ -lactams except monobactams, and evade all ⁇ -lactam inhibitors.
  • Plasmid-mediated IMP-type carbapenemases 48 varieties (IMP 1-IMP48) of which are currently known, became established in Japan in the 1990s both in enteric Gram-negative organisms and in Pseudomonas and Acinetobacter species. IMP enzymes spread slowly to other countries in the Far East, were reported from Europe in 1997, and have been found in Canada and Brazil.
  • carbapenems including imipenen and meropenem
  • penicillims monobactams
  • fluroquinones i.e. ciprofloxacin
  • cephalosporins i.e. cephalorodin, cefoxitin, cefepime
  • aminoglycosides i.e. amikacin
  • OXA beta-lactamases were long recognized as a less common but also plasmid-mediated beta-lactamase variety that could hydrolyze oxacillin and related anti-staphylococcal penicillins. These beta-lactamases differ from the TEM and SHV enzymes in that they belong to molecular class D and functional group 2d.
  • the OXA-type beta-lactamases confer resistance to ampicillin and cephalothin and are characterized by their high hydrolytic activity against oxacillin and cloxacillin and the fact that they are poorly inhibited by clavulanic acid. Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. While most ESBLs have been found in E. coli, K.
  • OXA-type ESBLs have been found in P. aeruginosa and Acinetobacter buamannii .
  • OXA-type ESBLs have been found mainly in Pseudomonas aeruginosa isolates from Turkey and France.
  • the OXA beta-lactamase family was originally created as a phenotypic rather than a genotypic group for a few beta-lactamases that had a specific hydrolysis profile. Therefore, there is as little as 20% sequence homology among some of the members of this family. However, recent additions to this family show some degree of homology to one or more of the existing members of the OXA beta-lactamase family. Some confer resistance predominantly to ceftazidime, but OXA-17 confers greater resistance to cefotaxime and cefepime than it does resistance to ceftazidime.
  • Plasmid encoded oxacillinase family i.e. OXA-2, OXA-15 and OXA-32
  • OXA-2, OXA-15 and OXA-32 Plasmid encoded oxacillinase family (i.e. OXA-2, OXA-15 and OXA-32), identified in Salmonella typhimurium and Pseudomonas aeruginosa clinical isolates in Europe. Hydrolyzes benzylpenicillin, penicillim, ampicillim, oxacillim, cephaloridine, cephalothin, and ceftazidime (hydrolysis rates varies within the family members). Well-inhibited by azobactam, but weakly inhibited by clavulanic acid.
  • Plasmid-encoded oxacillinase family i.e. OXA-14, OXA-16, and OXA-17
  • OXA-14, OXA-16, and OXA-17 Plasmid-encoded oxacillinase family (i.e. OXA-14, OXA-16, and OXA-17), identified in Pseudomonas aeruginosa clinical isolates in Europe. Hydrolyzes penicillim, ampicillim, cabenicillim, cloaxicillim, oxacillim, and cephaloridine, cefotaxime, ceftriaxone among others (hydrolysis rates varies within the family members).
  • Chromosomal-encoded oxacillinase identified in Pseudomonas aeruginosa clinical isolates in Europe. Shares weak identity with all class D ⁇ -lactamase except OXA-9 and OXA-12. Hydrolyzes amoxicillin, ticarcillin, cephalothin, ceftazidime, cefotaxime, and aztreonam, but not imipenem or cephamycins.
  • Chromosomal-encoded oxacillinase identified in Acinobacter bumannii in clinical isolates in Europe. Shows distant homology with OXA-10, OXA-7, and OXA-11. Hydrolyzes benzylpenicillin, ampicillin, cephaloridine, tircarcilin, imipenem and meropenem, but lack activity against oxacillin, cloxacillin and methicillim. Inhibited by NaCl, tazobactam, sulbactam and clavulanic acid.
  • Plasmid-encoded oxacillinase carried in Pseudomonas aeruginosa clinical strains in North America. Shares some enzyme homology with OXA-18, OXA-9, OXA-22, OXA-12 and OXA-29. Hydrolyzes ceftazidime, aztreonam (high levels), and cefotaxime (low level). Inhibited by NaCl, imipenem, and clavulanic acid.
  • Plasmid-encoded oxacillinase carried in Klebsiella pneumoniae clinical strains in Turkey. Remotely related to other oxacillinases. Hydrolyzes carbapenems at a level much higher than other oxacillinases as well as penicillims and imipenes, but not expanded-spectrum cephalosporins. Well-inhibited by NaCL and weakly inhibited by clavulanic acid, tazobactam, and sulbactam.
  • Chromosomal-encoded oxacillinase identified in Pseudomonas aeruginosa clinical strains in Europe. Hydrolyzes ampicillim, benzylpenicillin, cephaloridine, cephalothin, nitrocefin, piperacillin, and iminipen to low levels, but not oxackillin or cloxacillin. Hydrolyzes ampicillin, benzylpenicillin, cephaloridine, cephalothin, nitrocefin, piperacillin and imipenem (low level).
  • Chromosomal-encoded oxacillinase identified in Klebsiella pneumoniae, Acinobacter bumannii isolates in North and South America, Europe, and Asia. Hydrolyzes imipenem, cefepime, ceftazidime, piperacillin, piperacillin/tazobactam, aztreonam, ciprofloxacin and amikacin.
  • Chromosome-encoded oxacillinase identified in Shewanella algae clinical isolates in Europe. No significant identity exists between OXA-55 and other oxacillinases. Hydrolyzes benzylpenicillim, amplicillin amoxicillin, ticarcillin, peperacillin, oxacillin, cloxacillin, cephalothin, cephaloridine, cepirone, and iminipen and meropen (low levels). Inhibited by clavulanic acid, tazobactam, and sulbactam.
  • Plasmid-encoded oxacillinase carried in Acinobacter baumannii, Acinobacter junii and Acinobacter spp. clinical isolates in North South America, Europe, Asia, and Oceania. Weakly related to other oxacillinase genes. Hydrolyzes penicillins, oxacillin, and imipenem (low levels), but not ceftazidime, cefotaxime, and cefepime. Weakly inhibited by clavulanic acid, tazobactam, and sulbactam.
  • Chromosome-encoded oxacillinase identified in Ralstonia pickettii strains in Europe. Shows a greater homology with OXA-50 than other oxacillinases. Hydrolyzes benzylpenicillin, amoxicillin, piperacillin, ticarcillin, nitrocefin, oxacillin, cloxacillin. Well-inhibited by NaCl, but weakly inhibited by clavulanic acid, and tazobactam.
  • Chromosome-encoded oxacillinase identified in Pandoraea pnomenusa clinical strains. Shows a greater homology with OXA-50 than other oxacillinases. Hydrolyzes penicillins, oxacillin, imipenem, and meropenem, but not expanded-spectrum cephalosporins. Well-inhibited by NaCl, but weakly inhibited by clavulanic acid, and tazobactam.
  • Van-A, Van-B, Van-C, Van-D, Van-E and Van-F Six different types of vancomycin resistance are shown by enterococcus : Van-A, Van-B, Van-C, Van-D, Van-E and Van-F. Of these, only Van-A, Van-B and Van-C have been seen in general clinical practice, so far. The significance is that Van-AVRE is resistant to both vancomycin and teicoplanin.
  • the mechanism of resistance to vancomycin found in enterococcus involves the alteration to the terminal amino acid residues of the NAM/NAG-peptide subunits, under normal conditions, D-alanyl-D-alanine, to which vancomycin binds.
  • the D-alanyl-D-lactate variation results in the loss of one hydrogen-bonding interaction (four, as opposed to five for D-alanyl-D-alanine) being possible between vancomycin and the peptide. This loss of just one point of interaction results in a 1000-fold decrease in affinity.
  • the D-alanyl-D-serine variation causes a six-fold loss of affinity between vancomycin and the peptide, likely due to steric hindrance.
  • Plasmid-mediated AmpC type ⁇ -lactamase (cephalosporinases), carried in Klebsiella pneumonia, Escherichia coli, Proteus mirabilis , and Salmonella spp. in Europe and Africa. Shows distant amino acid sequence homology with known AmpC ⁇ -lactamases. Closely related to the chromosomally encoded AmpC-type ⁇ -lactamase of Hafnia alvei .
  • ACT-1 and MIR-1 are both plasmid-mediated AmpC type ⁇ -lactamases (Cephamycinases), carried in Escherichia coli and Klebsiella pneumonia in the US.
  • ACT-1 is highly homologous with MIR-1 and both ACT-1 and MIR-1 share high homology with the chromosomal ampC genes of Enterobacter cloacae .
  • ACT-1 hydrolyzes cefepime and cefoxitin.
  • MIR-1 hydrolyzes cephalothin, ceftazidime, cefoxitin, cefotetan, cefmetazole, moxalactam, aztreonam, ampicillin and carbenicillin.
  • CMY-2 and CFE-1 are both plasmid-mediated AmpC type ⁇ -lactamases (Cephamycinases), carried in Escherichia coli and Klebsiella pneumonia in Asia and Europe.
  • CMY-2 is highly homologous with CFE-1 and BIL-1, and both CMY-2 and CFE-1 share high homology with CMY-3/-4, LAT-1/-3 and the chromosomal ampC genes of Citrobacter freundii .
  • CMY-2 hydrolyzes cefoxitin, cefotetan, ceftibuten, aztreonam, and flomoxef.
  • CFE-1 hydrolyzes cephalothin and cefpodoxime. Both CMY-2 and CFE-1 hydrolyze ceftazidime, cefotaxime, piperacillin, and cefametazole.
  • Plasmid-mediated AmpC type ⁇ -lactamase (Cephalosporinase), carried in Salmonella enteritidis clinical isolates in Saudi Arabia. Highly homologous with the chromosome-mediated cephalosporinase of M. morganii . Hydrolyzes amoxicillim, amoxicillin plus clavulanic acid, ticarcillin, cephalothin, cefoxitin, cefoxatime, ceftazidime, and moxalactam, but not iminipen. Inhibited by low concentrations of aztreonam, cefoxitin, or cloxacillin and only by high concentrations of clavulanic acid.
  • Plasmid-mediated AmpC type ⁇ -lactamase (cephalosporinases), carried in Klebsiella pneumonia in Argentina. Highly homologous with FOX-2/-3. Hydrolyzes ampicillin, carbenicillin, cephalothin, cephaloridine, ceftazidime, cefotaxime, cefoxitin, cefotetan, and cefmetazole. Well-inhibited by cloxacillin and aztreonam, but poorly inhibited by clavulanic acid, tazobactam, and sulbactam.
  • Plasmid- and integron-encoded ⁇ -lactamase carried in Klebsiella pneumoniae clinical isolates in France. Hydrolyzes penicillins and expanded-spectrum cephalosporins, but not cephamycins, carbapenems, and aztreonam. Inhibited by clavulanate, tazobactam and imipenem.
  • IMI-1 and NMCA-1 are both chromosomal-encoded- ⁇ -lactamases, identified in Enterobacter cloacae clinical isolates in North America and Europe. IMI-1 shares high homology with the NMC-A and NMC-R genes, and may be considered NMC-type ⁇ -lactamase. IMI-1 hydrolyses cefotaxime and ceftazidime less fast than NMC-A, imipenem (high levels) and benzylpenicillin (modest rates), but more slowly than cephaloridine. NMCA-1 also hydrolyzes ampicillin, amoxicillin-clavulanic acid, cefazolin, and cefoxitin. In contrast to NMCA-1, IMI-1 is inhibited more effectively by tazobactam than by clavulanic acid.
  • CMY-1 (Cephamycinase), and MOX-1/MOX-5 (moxalactamases) are all plasmid-mediated AmpC type ⁇ -lactamases, carried in Escherichia coli and Klebsiella pneumonia in Asia and Africa.
  • CMY-1 shares high homology with MOX-1/MOX-5, and all of them are highly homologous with both FOX-1 and the chromosomal AmpC ⁇ -lactamase of Pseudomonas aeruginosa .
  • CMY-1 hydrolyzes cefoxitin, ceftriaxone, cefotaxime, Cefametazole, cefotetan, flomoxef, gentamicin, amikacin, nalidixic acid, ciprofloxacin, norfloxacin, piperacillin, and co-trimoxazole to a lesser extent.
  • MOX-1/MOX-5 hydrolyzes ampicillim, cefotaxine, aztreonam, and cefotetan. CMY-1 and MOX-1/MOX-5 are inhibited by clavulanic acid, sulbactam and tazobactam.
  • Plasmid-encoded ⁇ -lactamase carried in Pseudomonas aeruginosa, Acinetobacter spp., A. baumannii, Salmonella enterica serovar Typhimurium and Providencia rettgeri, P. stuartii and Proteus mirabilis in Europe and Asia. Shares significant homology with VEB-1 and TLA-1 enzymes, which belong to the ‘Per-like family’. Hydrolyzes penicillins, cefotaxime, ceftazidime, and aztreonam, but spares carbapenems and cephamycins. Well-inhibited by clavulanic acid, sulbactam and tazobactam.
  • Chromosomal-encoded- ⁇ -lactamase identified in Serratia fonticola strains from hospitals in Europe. Hydrolyzes penicillins, cephalosporins, aztreonam, and carbapenems and is inhibited by clavulanic acid, sulbactam, and tazobactam. Less inhibited by class A ⁇ -lactamase inhibitors than other group of carbapenemases.
  • Plasmid-encoded SHV-type extended spectrum ⁇ -lactamase harboring mutation G38S (glycine at position 238 in SHV-1 is replaced by serine in SHV-2, -3, -20, -21, -30, -34, -39, -106, -141, -152, -153, -162, and -163). Carried mainly in Klebsiella pneumonia, Escherichia coli, Serratia marcescens and Salmonella typhimurium in Europe, Asia and South-Africa.
  • SHV-2 hydrolyzes cefoxitin, cefotaxime, ceftazidime, ceftazidime-clavulanate, piperacillin-tazobactam, meropenem (high levels) and imipenem (intermediate level).
  • SHV-type extended spectrum ⁇ -lactamase harboring mutation E240K (glutamic acid at position 240 in SHV-1 replaced by lysine in SHV-31, -91, -97, -115, and -120). Carried mainly in Klebsiella pneumonia clinical strains in Europe. SHV-31 hydrolyzes ceftazidime, cefotaxime, and aztreonam, gentamicin, ciprofloxacin, and levofloxacin, but not cefepime and amikacin. Inhibited by clavulanic acid.
  • Plasmid-encoded SHV-type extended spectrum ⁇ -lactamase harboring double mutation G238S and E240K (glycine at position 238 and glutamic acid at position 240 in SHV-1 is replaced by serine and lysine, respectively in SHV-4, -5, -6, -7, -8, -9, -10, -12, -15, -22, -23, -45, -46, -55, -64, -66, -90, -105, -123, -124, -128, -129, 134, -154, -160, -165 and -183). Carried mainly in Klebsiella pneumonia, Enterobacter spp.
  • SHV-5 hydrolyzes amoxicillin, ticarcillin, piperpacillin, cephalexin, cephalothin, cefamandole, cefatzidime, ceftazidime, aztreonam, tigernoman (high levels) plus caruomonan and cefoxitin (intermediate levels). Inhibited by clavulanic acid, sulbactam and tazobactam.
  • Plasmid-encoded SHV-type extended spectrum beta-lactamase harboring mutation G156D Glycine at amino acid position 156 in SHV-1 replaced by aspartic acid in SHV-27, -32, -45, -93, -105, -110 and -177. Hydrolyzes amoxicillin, gentamicin, cefotaxime, ceftazidime, aztreonam and trimethoporim. Inhibited by clavuanic acid (Corkill et al, 2001). Carried by Klebsiella pneumonia in South America and Europe.
  • Plasmid-encoded metallo- ⁇ -lactamases carried in Pseudomonas aeruginosa clinical strains from Brazil. Represents a subfamily of mobile metallo- ⁇ -lactamase different from VIM and IMP. Hydrolyzes cloxacillin, oxacillin, penicillin, ampicillin, imipenem, meropenem, cefaloridine, ceftazidime and nitrocefin, and no inhibitor is clinical available.
  • Plasmid-encoded transposable element ⁇ -lactamase TEM-1 parental type Possesses glutamic acid at position 104. Commonly found in gram negative bacteria, mainly in Escherichia coli and Klebsiella pneumoniae . Hydrolyzes 90% of the penicillim-type antibiotics. Inhibited by clavuanic acid.
  • Plasmid-encoded TEM-type extended spectrum ⁇ -lactamase harboring mutation E104K (glutamic acid at position 104 in TEM-1 replaced by lysine in TEM-3, -4, -6, -8, -9, -15, -16, -17, -18, -21, -22, -24, -26, among other 39 more TEM-type variants). Carried mainly in Klebsiella pneumoniae, Escherichia coli, Salmonella typhimurium, Salmonella spp. in North America, Europe and Africa.
  • TEM-3 hydrolyzes amikacin, netilmicin, tobramycin, tetracycline, sulphonamides ampicillim and gentamycin (high levels) plus trimethoprim-sulfamethoxazole (low level).
  • Plasmid-encoded transposable element ⁇ -lactamase TEM-1 parental type Possesses arginine acid at position 164. Commonly found in gram negative bacteria, mainly in Escherichia coli and Klebsiella pneumoniae . Hydrolyzes 90% of the penicillim-type antibiotics. Inhibited by clavuanic acid. Carried mainly in Klebsiella pneumoniae and Escherichia coli in North America and Europe.
  • Plasmid-encoded TEM-type extended spectrum ⁇ -lactamase harboring mutation R164H arginine acid at position 104 in TEM-1 replaced by histidine in TEM-6, -11, -16, -27, -28, -29, -43, -61, -75, -107, -109, -115, -118, -132, -134, -147, -151, -152, -161, and -187).
  • TEM-115 hydrolyses ceftazidime, gentamicin and tobramycin (moderate levels). Inhibited by clavuanic acid (low level).
  • Plasmid-encoded TEM-type extended spectrum ⁇ -lactamase harboring mutation R164C arginine acid at position 104 in TEM-1 replaced by asparatic acid in TEM-87, -91, -143, -144, -193, and -195. Carried mainly in Klebsiella pneumoniae, Escherichia coli , and Proteus mirabilis in Europe.
  • TEM-87 hydrolyzes ampicillin, amoxicillin-clavulanate, piperacillin, cefazolin, ceftazidime, cefepime and aztreonam. Inhibited by clavuanic acid.
  • Plasmid-encoded TEM-type extended spectrum ⁇ -lactamase harboring mutation R164S arginine acid at position 104 in TEM-1 replaced by serine in i.e. TEM-5, -7, -8, -9, -10, -12, -24, -26, -46, -53, -60, -85, -86, -102, -114, -121, -125, -129, -130, -131, -133, -136, -137, -149, -154, -155, -158, -165, -177, -184, and -205).
  • TEM-7 hydrolyzes ampicillin, piperacillin, ceftazidime and aztreonam but not other third-generation cephalosporins. Inhibited by clavuanic acid.
  • Plasmid-encoded transposable element ⁇ -lactamase TEM-1 parental type Possesses glycine at position 238 and glutamic acid at 240 position. Commonly found in gram negative bacteria, mainly in Escherichia coli and Klebsiella pneumoniae . Hydrolyzes 90% of the penicillim-type antibiotics. Inhibited by clavuanic acid.
  • Plasmid-encoded TEM-type extended spectrum ⁇ -lactamase harboring mutation E240K (glutamic acid at position 240 in TEM-1 replaced by lysine in TEM-5, -10, -24, -27, -28, -46, -61, -85, -86, -91, -114, -121, -136, -144, -152, -155, -177, and -191). Carried mainly in Klebsiella pneumoniae in the US. TEM-10 hydrolyzes cephaloridine, benzylpenicillim, amipicillim, piperacillin, ceftazidime, and aztreonam. Inhibited by p-chloromercuribenzoate.
  • Plasmid-encoded TEM-type extended spectrum ⁇ -lactamase harboring mutation G38S glycine at position 238 in TEM-1 is replaced by serine in TEM-3, -4, -8, -15, -19, -20, -21, -22, -25, -50, -52, -66, -88, -89, -92, -94, -107, -112, -113, -120, -123, -134, -138, -139, -167, -197, -199, and -211). Carried mainly in Klebsiella pneumoniae and Escherichia coli in Asia. TEM-19-20, and -52 hydrolyzes ampicillin, cephalothin, ceftazidime, and aztreonam, and cefotaxime.
  • Plasmid-encoded TEM-type extended spectrum ⁇ -lactamase harboring double mutation G238S and E240K (glycine at position 238 and glutamic acid at position 240 in TEM-1 is replaced by serine and lysine, respectively in TEM-42, -47, -48, -49, -68, -71, -72, -93, -101, and -188). Carried mainly in Klebsiella pneumoniae and Pseudomonas aeruginosa in Europe.
  • TEM-42 hydrolyzes penicillim, cephaloridine, and cefotaxime. Inhibited by clavuanic acid.
  • Plasmid- and integron-encoded ⁇ -lactamase carried in clinical strains in Pseudomonas aeruginosa, P. stuartii Escherichia coli, Acinetobacter baumannii isolates, Providencia stuartii, Enterobacter cloacae and A. xylosoxidans isolates in South America, Africa, Asia, and Europe. Shares some enzyme homology with PER-1 and -2. Hydrolyzes ceftazidime, cefotaxime, aztreonam and quinolones (high levels) plus penicillim (low levels). Inhibited by clavulanate, sulbactam and tazobactam, moxalactam, imipenem and cefoxitin.
  • the genes detected that confer multi-gene resistance are referred to herein as MDRO-associated genes or resistome genes and encompass one or more genes or gene families of KPC, NDM, VIM, IMP, OXA, CTX-M, Van-A, IMI, SME, GIM, SPM, NMC, SFC, SHV, TEM, BEL, VEB, GES, PER, SFC, BES, TLA, ACC, CMY, MIR, ACT, DHA, MOX, FOX, or CFE.
  • the genes includes all family members.
  • KPC it is meant to include KPC 2-KPC-16.
  • OXA it is meant to include OXA-48, 23, 51, 2, 10, 18, 24, 45, 50, 54, 55, 58, 60, and 62.
  • Exemplary MDRO-associated genes useful in the practice of the methods of invention include but are not limited to the genes listed on Table 1.
  • a gene abbreviation e.g. KPC, OXA, VIM, etc
  • KPC it is meant to include at least one and up to all subtypes.
  • KPC-2 it is meant to include at least one and up to all subtypes (e.g. KPC-2 through KPC-16) of KPC.
  • the gene abbreviation is followed by a number (e.g., VIM-1, VIM-5, OXA-2).
  • OXA-2 it is meant to include OXA-2, 15, 32.
  • the method involves extraction of bacterial DNA from a biological sample from a patient or directly from a biological sample culture or culture isolate. Extraction can be accomplished by any known method in the art. Preferably, the extraction method both isolates and purifies the DNA. By “purifies” it is meant that DNA sample is substantially free of protein, cellular debris and PCR inhibitors. Methods of extraction suitable for use in the present invention include, for example but not limited to Roche MagNAPure.
  • the methods of the invention provide ultra-high sensitivity and resolution of MDRO-associated genes, with format flexibility to discriminate individual gene subtypes, or to screen for all MDRO gene families and subtypes in a combined probe “cocktail” assay format.
  • the method provides for an optimal assay system whereby new MDRO genes or subtypes or infectious disease organism molecular biomarkers or identification genes can be incorporated into the assay format, to expand the scope of MDRO screening and identification potential based on the emergence of new MDROs over time.
  • This ultra-high sensitivity and resolution may be accomplished with or without combining a pre-amplification step followed by a detection step utilizing primers and probes based upon sequence homology of the MRDO-associated gene families.
  • primers and probes include degenerate primers sequence capable of amplifying and detecting MDRO associated gene sub-families and subtypes, and based on the level of detection, can provide a semi-quantitative assessment on the level of MDRO genes in the sample.
  • the methods of the invention are not only capable of detecting the presence of a MRDO-associated gene in a sample, the method also provides for the identification and semi-quantitative level of the subtype of the MDRO-associated gene. This ability to provide a genotype allows for the presumptive identification of bacterial or other infectious disease species.
  • an unexpected advantage of the methods of the invention is that it provides the clinician with some guidance as to which bacteria species the subject is infected/or colonized with, and provides guidance on the risk profile of the subject for potential conversion from colonization to infection, or potential risk of transmitting a MDRO to another individual. (See, FIG. 1 ). It is also possible to include probes in the test format for organism identification (ID) and viruses along with Resistome Test probes to provide additional information about the patient microbiome. It is also possible to perform sequence-based microbiome analysis along with the Resistome Test.
  • ID organism identification
  • Resistome Test sequence-based microbiome analysis along with the Resistome Test.
  • the Resistome Test can be used by a clinician to help determine which antibiotics should be used based on a Resistome test result of the patient sample, either because of an individual resistance gene or combination of genes. Overall, the ability to stratify genotype is also very specific and reproducible (See, FIGS. 3 and 4 ). Organism Resistome profiles can be matched with actual Antibiotic Susceptibility Test (AST) data. When patients with matching Resistome patterns are found, their antibiotic resistance can potentially be inferred from this information.
  • AST Antibiotic Susceptibility Test
  • Another unexpected advantage of the methods of the invention is the extreme sensitivity that can be ascertained from different sample types, including using a single swab sample, mixed culture sample, or bacterial isolate. Unlike other methods known in the art, the methods of the invention are capable of detecting less than 210 CFU/sample (and in some instance less than 15 CFU/sample) without the need to culture the sample. (See, FIG. 2 ).
  • the patient is suspected of or at high risk for having a multi-drug resistant bacteria colonization or infection.
  • High risk patients include but are not limited to, patients residing in or being admitted from a long-term care facility, patients admitted to Intensive Care Units (ICUs), immuno-compromised patients, patients being treated for cancer or undergoing chemotherapy, organ and bone marrow transplant patients, patients with ventilators or catheters, patients in preparation for surgical procedures, postsurgical patients, patients previously diagnosed or treated for a Healthcare-Associated Infection (HAI), and others.
  • a high risk patient is neutropenic, has cancer or has received a transplant.
  • the patient is “asymptomatic” means not exhibiting the traditional signs and symptoms.
  • the sample is any biological sample that contains gram-negative or gram-positive bacteria.
  • the biological sample is an anal swab, a rectal swab, a skin swab, nasal swab, wound swab, stool, blood, plasma, serum, urine, sputum, respiratory lavage, cerebrospinal fluid, or culture isolate.
  • an enrichment step is performed prior to the detection of the MDRO associated genes. Enrichment is accomplished for example by performing multiplex PCR. After enrichment, detection is performed for example by using real time PCR using primers that are specific to the MDRO associated gene being detected. Optionally, an internal amplification control is included to guard against false negatives associated with PCR inhibition. Additionally, appropriate positive, negative and no-template control (NTC) samples are included during each performance run of the assay.
  • NTC no-template control
  • infection is meant to include any infectious agent of bacterial origin.
  • the bacterial infection may be the result of gram-positive, gram-negative bacteria or atypical bacteria.
  • Gram-positive bacteria are bacteria that are stained dark blue by Gram staining Gram-positive organisms are able to retain the crystal violet stain because of the high amount of peptidoglycan in the cell wall.
  • Gram-negative bacteria are bacteria that do not retain the crystal violet dye in the Gram staining protocol.
  • Multi-drug Resistant Organism is a microrganisms (bacteria, viruses, fungi or parasites) that is resistant to distinct antimicrobial agents, first and foremost antibiotics, but also antifungal drugs, antiviral medications, and antiparasitic drugs.
  • CRE refers to carbapenem-resistant enterobacteriaceae.
  • ESBL refers to extended spectrum beta lactamase.
  • AmpC refers to cephalosporinases encoded on the chromosomes of many of the Enterobacteriaceae and a few other organisms, where they mediate resistance to cephalothin, cefazolin, cefoxitin, most penicillins, and beta-lactamase inhibitor-beta-lactam combinations.
  • a multi-drug resistant organism includes, but are not limited to, organisms belonging to the genus Acinetobacter, Citrobacter, Enterobacter, Enteroccus, Escherichia, Kiebsiella, Serratia or Staphyloccus .
  • Exemplary multi-drug resistant organisms include Acinetobacter Baumannii such as ATCC isolate #2894233-696-101-1, ATCC isolate #2894257-696-101-1 ATCC isolate #2894255-696-101-1, ATCC isolate #2894253-696-101-1, or ATCC #2894254-696-101-1; Citrobacter freundii such as ATCC isolate #33128, ATCC isolate #2894218-696-101-1, ATCC isolate #2894219-696-101-1, ATCC isolate #2894224-696-101-1, ATCC isolate #2894218-632-101-1, or ATCC isolate #2894218-659-101-1; Enterobacter cloacae such as ATCC isolate #22894251-659-101-1, ATCC isolate #22894264-659-101-1, ATCC isolate #22894246-659-101-1, ATCC isolate #22894243-659-101-1, or ATCC isolate #22894245-659-101-1 ; Enteroccus facalis such as
  • methods of treating includes methods of managing, and when used in connection with the biological organism or infection, includes the amelioration, elimination, reduction, prevention, or other relief or management from the detrimental effects of a biological organism.
  • these detrimental effects include a mycobacterial infection, symptoms characterizing and/or effects associated with tuberculosis in the subject, or a combination thereof
  • nucleic acid includes one or more types of: polydeoxyribonucleotides (containing 2-deoxy-D-ribose), polyribonucleotides (containing D-ribose), and any other type of polynucleotide that is an N-glycoside of a purine or pyrimidine base, or modified purine or pyrimidine bases (including abasic sites).
  • nucleic acid also includes polymers of ribonucleosides or deoxyribonucleosides that are covalently bonded, typically by phosphodiester linkages between subunits, but in some cases by phosphorothioates, methylphosphonates, and the like. “Nucleic acids” include single- and double-stranded DNA, as well as single- and double-stranded RNA.
  • nucleic acids include, without limitation, gDNA; hnRNA; mRNA; rRNA, tRNA, micro RNA (miRNA), small interfering RNA (siRNA), small nucleolar RNA (snORNA), small nuclear RNA (snRNA), and small temporal RNA (stRNA), and the like, and any combination thereof
  • DNA segment refers to a DNA molecule that has been isolated free of total genomic DNA of a particular species. Therefore, a DNA segment obtained from a biological sample using one of the compositions disclosed herein refers to one or more DNA segments that have been isolated away from, or purified free from, total genomic DNA of the particular species from which they are obtained, and also in the case of pathogens, optionally isolated away from, or purified free from total mammalian (preferably human) genomic DNA of the infected individual. Included within the term “DNA segment,” are DNA segments and smaller fragments of such segments, as well as recombinant vectors, including, for example, plasmids, cosmids, phage, viruses, and the like.
  • RNA segment refers to an RNA molecule that has been isolated free of total cellular RNA of a particular species. Therefore, RNA segments obtained from a biological sample using one of the compositions disclosed herein, refers to one or more RNA segments (either of native or synthetic origin) that have been isolated away from, or purified free from, other RNAs. Included within the term “RNA segment,” are RNA segments and smaller fragments of such segments.
  • nucleic acid or polypeptide sequences refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence, as measured using one of the sequence comparison algorithms described below (or other algorithms available to persons of ordinary skill) or by visual inspection.
  • nucleic acids refers to two or more sequences or subsequences that have at least about 90%, preferably 91%, most preferably about 92%, 93%, 94%, 95%, 96%, 97%, 98%, 98.5%, 99%, 99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% or more nucleotide residue identity, when compared and aligned for maximum correspondence, as measured using a sequence comparison algorithm or by visual inspection.
  • Such “substantially identical” sequences are typically considered “homologous,” without reference to actual ancestry.
  • sample includes anything containing or presumed to contain a substance of interest. It thus may be a composition of matter containing nucleic acid, protein, or another biomolecule of interest.
  • sample can thus encompass a solution, cell, tissue, or population of one of more of the same that includes a population of nucleic acids (genomic DNA, cDNA, RNA, protein, other cellular molecules, etc.).
  • nucleic acid source “sample,” and “specimen” are used interchangeably herein in a broad sense, and are intended to encompass a variety of biological sources that contain nucleic acids, protein, one or more other biomolecules of interest, or any combination thereof.
  • Exemplary biological samples include, but are not limited to, whole blood, plasma, serum, sputum, urine, stool, white blood cells, red blood cells, buffy coat, swabs (including, without limitation, buccal swabs, throat swabs, vaginal swabs, urethral swabs, cervical swabs, rectal swabs, lesion swabs, abscess swabs, nasopharyngeal swabs, and the like), urine, stool, sputum, tears, mucus, saliva, semen, vaginal fluids, lymphatic fluid, amniotic fluid, spinal or cerebrospinal fluid, peritoneal effusions, pleural effusions, exudates, punctates, epithelial smears, biopsies, bone marrow samples, fluids from cysts or abscesses, synovial fluid, vitreous or aqueous humor, eye washes or aspirates, bronchi
  • Tissue culture cells including explanted material, primary cells, secondary cell lines, and the like, as well as lysates, homogenates, extracts, or materials obtained from any cells, are also within the meaning of the term “biological sample,” as used herein.
  • biological sample as used herein.
  • lysates, extracts, or materials obtained from any of the above exemplary biological samples are also within the scope of the invention.
  • buffer includes one or more compositions, or aqueous solutions thereof, that resist fluctuation in the pH when an acid or an alkali is added to the solution or composition that includes the buffer. This resistance to pH change is due to the buffering properties of such solutions, and may be a function of one or more specific compounds included in the composition. Thus, solutions or other compositions exhibiting buffering activity are referred to as buffers or buffer solutions. Buffers generally do not have an unlimited ability to maintain the pH of a solution or composition; rather, they are typically able to maintain the pH within certain ranges, for example from a pH of about 5 to 7.
  • the term “patient” refers to any host that can serve as a source of one or more of the biological samples or specimens as discussed herein.
  • the donor will be a vertebrate animal, which is intended to denote any animal species (and preferably, a mammalian species such as a human being).
  • a “patient” refers to any animal host, including but not limited to, human and non-human primates, avians, reptiles, amphibians, bovines, canines, caprines, cavities, corvines, epines, equines, felines, hircines, lapines, leporines, lupines, ovines, porcines, racines, vulpines, and the like, including, without limitation, domesticated livestock, herding or migratory animals or birds, exotics or zoological specimens, as well as companion animals, pets, and any animal under the care of a veterinary practitioner.
  • substantially free typically means that a composition contains less than about 10 weight percent, preferably less than about 5 weight percent, and more preferably less than about 1 weight percent of a compound. In a preferred embodiment, these terms refer to less than about 0.5 weight percent, more preferably less than about 0.1 weight percent or even less than about 0.01 weight percent. The terms encompass a composition being entirely free of a compound or other stated property, as well. With respect to degradation or deterioration, the term “substantial” may also refer to the above-noted weight percentages, such that preventing substantial degradation would refer to less than about 15 weight percent, less than about 10 weight percent, preferably less than about 5 weight percent, etc., being lost to degradation.
  • these terms refer to mere percentages rather than weight percentages, such as with respect to the term “substantially non-pathogenic” where the term “substantially” refers to leaving less than about 10 percent, less than about 5 percent, etc., of the pathogenic activity.
  • heterologous is defined in relation to a predetermined referenced nucleic acid sequence.
  • a heterologous promoter is defined as a promoter that does not naturally occur adjacent to the referenced structural gene, but which is positioned by the hand of man in one or more laboratory manipulations that are routinely employed by those of ordinary skill in the molecular biological arts.
  • a heterologous gene or nucleic acid segment is defined as a gene or nucleic acid segment that does not naturally occur adjacent to the referenced sequence, promoter and/or enhancer element(s), etc.
  • the term “healthy” refers to an individual whom is not at high risk of being infected with a multi-drug resistant organism.
  • the term “homology” refers to a degree of complementarity between two or more polynucleotide or polypeptide sequences.
  • the word “identity” may substitute for the word “homology” when a first nucleic acid or amino acid sequence has the exact same primary sequence as a second nucleic acid or amino acid sequence.
  • Sequence homology and sequence identity can be determined by analyzing two or more sequences using algorithms and computer programs known in the art. Such methods may be used to assess whether a given sequence is identical or homologous to another selected sequence.
  • homologous means, when referring to polynucleotides, sequences that have the same essential nucleotide sequence, despite arising from different origins. Typically, homologous nucleic acid sequences are derived from closely related genes or organisms possessing one or more substantially similar genomic sequences. By contrast, an “analogous” polynucleotide is one that shares the same function with a polynucleotide from a different species or organism, but may have a significantly different primary nucleotide sequence that encodes one or more proteins or polypeptides that accomplish similar functions or possess similar biological activity. Analogous polynucleotides may often be derived from two or more organisms that are not closely related (e.g., either genetically or phylogenetically).
  • nucleic acid or polynucleotide sequences refer to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using a sequence comparison algorithm or by manual alignment and visual inspection.
  • a “primer” or “primer sequence” may include any nucleic acid sequence or segment that selectively hybridizes to a complementary template nucleic acid strand (“target sequence”) and functions as an initiation point for the addition of nucleotides to replicate the template strand.
  • Target sequence complementary template nucleic acid strand
  • Primer sequences of the present invention may be labeled or contain other modifications which allow the detection and/or analysis of amplification products.
  • primer sequences may also be used for the reverse transcription of template RNAs into corresponding DNAs.
  • target sequence or “target nucleotide sequence” as used herein includes any nucleotide sequence to which one of the disclosed primer sequences hybridizes under conditions that allow an enzyme having polymerase activity to elongate the primer sequence, and thereby replicate the complementary strand.
  • polypeptide is intended to encompass a singular “polypeptide” as well as plural “polypeptides,” and includes any chain or chains of two or more amino acids.
  • terms including, but not limited to “peptide,” “dipeptide,” “tripeptide,” “protein,” “enzyme,” “amino acid chain,” and “contiguous amino acid sequence” are all encompassed within the definition of a “polypeptide,” and the term “polypeptide” can be used instead of, or interchangeably with, any of these terms.
  • polypeptides that have undergone one or more post-translational modification(s), including for example, but not limited to, glycosylation, acetylation, phosphorylation, amidation, derivatization, proteolytic cleavage, post-translation processing, or modification by inclusion of one or more non-naturally occurring amino acids.
  • post-translational modification(s) including for example, but not limited to, glycosylation, acetylation, phosphorylation, amidation, derivatization, proteolytic cleavage, post-translation processing, or modification by inclusion of one or more non-naturally occurring amino acids.
  • Conventional nomenclature exists in the art for polynucleotide and polypeptide structures.
  • amino acids Alanine (A; Ala), Arginine (R; Arg), Asparagine (N; Asn), Aspartic Acid (D; Asp), Cysteine (C; Cys), Glutamine (Q; Gln), Glutamic Acid (E; Glu), Glycine (G; Gly), Histidine (H; His), Isoleucine (I; Ile), Leucine (L; Leu), Methionine (M; Met), Phenylalanine (F; Phe), Proline (P; Pro), Serine (S; Ser), Threonine (T; Thr), Tryptophan (W; Trp), Tyrosine (Y; Tyr), Valine (V; Val), and Lysine (K; Lys).
  • Amino acid residues described herein are preferred to be in the “L” isomeric form. However, residues in the “D” isomeric form may be substituted for any L-amino acid residue
  • Protein is used herein interchangeably with “peptide” and “polypeptide,” and includes both peptides and polypeptides produced synthetically, recombinantly, or in vitro and peptides and polypeptides expressed in vivo after nucleic acid sequences are administered into a host animal or human subject.
  • polypeptide is preferably intended to refer to all amino acid chain lengths, including those of short peptides of about 2 to about 20 amino acid residues in length, oligopeptides of about 10 to about 100 amino acid residues in length, and polypeptides of about 100 to about 5,000 or more amino acid residues in length.
  • sequence when referring to amino acids, relates to all or a portion of the linear N-terminal to C-terminal order of amino acids within a given amino acid chain, e.g., polypeptide or protein; “subsequence” means any consecutive stretch of amino acids within a sequence, e.g., at least 3 consecutive amino acids within a given protein or polypeptide sequence.
  • sequence and “subsequence” have similar meanings relating to the 5′ to 3′ order of nucleotides.
  • substantially homologous encompasses two or more biomolecular sequences that are significantly similar to each other at the primary nucleotide sequence level.
  • “substantially homologous” can refer to at least about 75%, preferably at least about 80%, and more preferably at least about 85%, or at least about 90% identity, and even more preferably at least about 95%, more preferably at least about 97% identical, more preferably at least about 98% identical, more preferably at least about 99% identical, and even more preferably still, entirely identical (i.e., 100% or “invariant”).
  • the term “substantially identical” encompasses two or more biomolecular sequences (and in particular polynucleotide sequences) that exhibit a high degree of identity to each other at the nucleotide level.
  • “substantially identical” can refer to sequences that at least about 80%, and more preferably at least about 85% or at least about 90% identical to each other, and even more preferably at least about 95%, more preferably at least about 97% identical, more preferably at least about 98% identical, more preferably at least about 99% identical, and even more preferably still, entirely identical (i.e., 100% identical or “non-degenerate”).
  • recombinant indicates that the material (e.g., a polynucleotide or a polypeptide) has been artificially or synthetically (non-naturally) altered by human intervention. The alteration can be performed on the material within or removed from, its natural environment or state. Specifically, e.g., a promoter sequence is “recombinant” when it is produced by the expression of a nucleic acid segment engineered by the hand of man.
  • a “recombinant nucleic acid” is one that is made by recombining nucleic acids, e.g., during cloning, DNA shuffling or other procedures, or by chemical or other mutagenesis
  • a “recombinant polypeptide” or “recombinant protein” is a polypeptide or protein which is produced by expression of a recombinant nucleic acid
  • a “recombinant virus,” e.g., a recombinant influenza virus is produced by the expression of a recombinant nucleic acid.
  • operably linked refers to a linkage of two or more polynucleotides or two or more nucleic acid sequences in a functional relationship.
  • a nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence.
  • a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the coding sequence.
  • “Operably linked” means that the nucleic acid sequences being linked are typically contiguous, or substantially contiguous, and, where necessary to join two protein coding regions, contiguous and in reading frame. Since enhancers generally function when separated from the promoter by several kilobases and intronic sequences may be of variable lengths; however, some polynucleotide elements may be operably linked but not contiguous.
  • isolated or “biologically pure” refer to material that is substantially, or essentially, free from components that normally accompany the material as it is found in its native state.
  • isolated polynucleotides in accordance with the invention preferably do not contain materials normally associated with those polynucleotides in their natural, or in situ, environment.
  • Link refers to any method known in the art for functionally connecting one or more proteins, peptides, nucleic acids, or polynucleotides, including, without limitation, recombinant fusion, covalent bonding, disulfide bonding, ionic bonding, hydrogen bonding, electrostatic bonding, and the like.
  • Plasmids of the present invention may include one or more genetic elements as described herein arranged such that an inserted coding sequence can be transcribed and translated in a suitable expression cells.
  • the plasmid may include one or more nucleic acid segments, genes, promoters, enhancers, activators, multiple cloning regions, or any combination thereof, including segments that are obtained from or derived from one or more natural and/or artificial sources.
  • Suitable standard hybridization conditions for the present invention include, for example, hybridization in 50% formamide, 5.times.Denhardts' solution, 5.times.SSC, 25 mM sodium phosphate, 0.1% SDS and 100.mu.g/mL of denatured salmon sperm DNA at 42 degrees C. for 16 h followed by 1 hr sequential washes with 0.1.times.SSC, 0.1% SDS solution at 60.degree. C. to remove the desired amount of background signal.
  • Lower stringency hybridization conditions for the present invention include, for example, hybridization in 35% formamide, 5.times.Denhardts' solution, 5.times.SSC, 25 mM sodium phosphate, 0.1% SDS and 100.mu.g/mL denatured salmon sperm DNA or E. coli DNA at 42 degrees C. for 16 h followed by sequential washes with 0.8.times.SSC, 0.1% SDS at 55.degree. C.
  • Those of skill in the art will recognize that conditions can be readily adjusted to obtain the desired level of stringency.
  • nucleic acid segments that are complementary, essentially complementary, and/or substantially complementary to at least one or more of the specific nucleotide sequences specifically set forth herein.
  • Nucleic acid sequences that are “complementary” are those that are capable of base-pairing according to the standard Watson-Crick complementarity rules.
  • complementary sequences means nucleic acid sequences that are substantially complementary, as may be assessed by the same nucleotide comparison set forth above, or as defined as being capable of hybridizing to one or more of the specific nucleic acid segments disclosed herein under relatively stringent conditions such as those described immediately above.
  • the probes and primers of the present invention may be of any length.
  • an algorithm defining all probes or primers contained within a given sequence can be proposed: n to n+y where n is an integer from 1 to the last number of the sequence and y is the length of the probe or primer minus one, where n+y does not exceed the last number of the sequence.
  • n is an integer from 1 to the last number of the sequence
  • y is the length of the probe or primer minus one, where n+y does not exceed the last number of the sequence.
  • the collection of probes or primers correspond to bases 1 to 25, bases 2 to 26, bases 3 to 27, bases 4 to 28, and so on over the entire length of the sequence.
  • exemplary primer or probe sequence include, without limitation, sequences corresponding to bases 1 to 35, bases 2 to 36, bases 3 to 37, bases 4 to 38, and so on over the entire length of the sequence.
  • probes or primers may correspond to the nucleotides from the first basepair to by 40, from the second by of the sequence to by 41, from the third by to by 42, and so forth
  • probes or primers may correspond to a nucleotide sequence extending from bp 1 to bp 50, from bp 2 to bp 51, from bp 3 to bp 52, from bp 4 to bp 53, and so forth.
  • nucleic acid segments of the present invention in combination with an appropriate detectable marker (i.e., a “label,”), such as in the case of employing labeled polynucleotide probes in determining the presence of a given target sequence in a hybridization assay.
  • an appropriate detectable marker i.e., a “label,”
  • a wide variety of appropriate indicator compounds and compositions are known in the art for labeling oligonucleotide probes, including, without limitation, fluorescent, radioactive, enzymatic or other ligands, such as avidin/biotin, etc., which are capable of being detected in a suitable assay.
  • an enzyme tag such as urease, alkaline phosphatase or peroxidase
  • colorimetric, chromogenic, or fluorigenic indicator substrates are known that can be employed to provide a method for detecting the sample that is visible to the human eye, or by analytical methods such as scintigraphy, fluorimetry, spectrophotometry, and the like, to identify specific hybridization with samples containing one or more complementary or substantially complementary nucleic acid sequences.
  • multiplexing assays where two or more labeled probes are detected either simultaneously or sequentially, it may be desirable to label a first oligonucleotide probe with a first label having a first detection property or parameter (for example, an emission and/or excitation spectral maximum), which also labeled a second oligonucleotide probe with a second label having a second detection property or parameter that is different (i.e., discreet or discernable from the first label.
  • first detection property or parameter for example, an emission and/or excitation spectral maximum
  • amplification primers and/or hybridization probes described herein will be useful both as reagents in solution hybridization (e.g., PCR methodologies and the like), and in embodiments employing “solid-phase” analytical protocols and such like.
  • the methods disclosed herein are used to identify subjects that are colonized or infected with a multi-drug resistant organism. More specifically, some methods of the invention are used to distinguish patients having a multi-drug resistant organism from patients with a non-infectious disease and/or healthy individuals. For example, the methods of the invention can be used to make a contact precaution recommendation for the patient having a multi-drug resistant bacterial colonization or infection. Contact precaution recommendations includes one or more of the following: isolating the patient to a quarantine area or ward, providing a private room for said patient, donning personal protective apparel upon entering the patient's room, limiting patient mobility, limiting or restricting access of non-colonized or non-infected patients or medical personnel to the patient, or providing dedicated patient care equipment.
  • Some methods of the present invention can also be used to monitor or select a treatment regimen for a patient who has an MDRO colonization or infection, and to screen subjects who have not been previously diagnosed as having an MDRO colonization or infection, such as subjects who exhibit risk factors for developing an infection. Some methods of the present invention are used to identify and/or diagnose subjects who are asymptomatic for a MDRO infection. “Asymptomatic” means not exhibiting the traditional signs and symptoms.
  • a reference value can be relative to a number or value derived from population studies, including without limitation, such subjects having the same infection, subject having the same or similar age range, subjects in the same or similar ethnic group, or relative to the starting sample of a subject undergoing treatment for an infection.
  • Such reference values can be derived from statistical analyses and/or risk prediction data of populations obtained from mathematical algorithms and computed indices of infection. Reference indices can also be constructed and used using algorithms and other methods of statistical and structural classification.
  • the effectiveness of a treatment regimen can be monitored by detecting a one or more MDRO-associated genes in a sample obtained from a subject over time and comparing the amount of MDRO-associated genes detected. For example, a first sample can be obtained prior to the subject receiving treatment and one or more subsequent samples are taken after or during treatment of the subject.
  • the methods of the invention can be used to discriminate between patients that are colonized or infected with an MDRO and those that are not. This will allow patients to be stratified and treated accordingly.
  • a treatment recommendation i.e., selecting a treatment regimen for a subject is provided by identifying a MDRO colonization or infection in the subject according to the method of any of the disclosed methods and recommending that the subject receive an antibiotic treatment.
  • the presence or absence of the MDRO-associated genes and are used in conjunction with other clinical factors that to make an antibiotic recommendation for a patient For example KPC, NDM, OXA, VIM, IMP, SME, SFC, IMI, NMC, or CcrA is detected consider that the patient may be resistant to carbapenem antibiotics; when CTM-X, PER, VEB, GES, BES, SFO, TLA, TEM with amino acid substitutions E104K, R164H, R164S, R164C, G238S or E240K, or SHV with amino acid substitutions G156D, G238S or E240K is detected consider that the patient may be resistant to cephalosporin antibiotics, when ACC, MOX, CMY, CFE, ACT, DHA or FOX is detected consider that the patient may be resistant to a beta-lactamase inhibitor-beta-lactam combination; or when VanA is consider that the patient may be resistant to vancomycin.
  • the methods of the invention can be used to prompt additional targeted diagnosis such as pathogen specific PCRs, chest-X-ray, cultures etc.
  • the methods of the invention can be used to recommend a test to determine the genus and or species of the multi-drug resistant organism to determine the source of the bacterial infection.
  • the methods of the invention can be used as a screening and surveillance method to establish the source and type of infection or colonization in a patient or person athlete (anatomical site) and/or from the environment such as hospital room location or fixture, or sports facility locker room location, in order to characterize infection transmission events and to generate geophysical maps of infection outbreaks in healthcare settings, sports complexes, and other physical settings where MDROs may colonize or spread (see FIGS. 7 , 8 , 9 , and 10 ).
  • Some aspects of the present invention can also be used to screen patient or subject populations in any number of settings.
  • a health maintenance organization, public health entity or school health program can screen a group of subjects to identify those requiring interventions, as described above, or for the collection of epidemiological data.
  • Insurance companies e.g., health, life or disability
  • Data collected in such population screens, particularly when tied to any clinical progression to conditions like infection, will be of value in the operations of, for example, health maintenance organizations, public health programs and insurance companies.
  • Such data arrays or collections can be stored in machine-readable media and used in any number of health-related data management systems to provide improved healthcare services, cost effective healthcare, improved insurance operation, etc. See, for example, U.S.
  • Such systems can access the data directly from internal data storage or remotely from one or more data storage sites as further detailed herein.
  • a machine-readable storage medium can comprise a data storage material encoded with machine readable data or data arrays which, when using a machine programmed with instructions for using said data, is capable of use for a variety of purposes.
  • Measurements of effective amounts of the biomarkers of the invention and/or the resulting evaluation of risk from those biomarkers can be implemented in computer programs executing on programmable computers, comprising, inter alia, a processor, a data storage system (including volatile and non-volatile memory and/or storage elements), at least one input device, and at least one output device.
  • Program code can be applied to input data to perform the functions described above and generate output information.
  • the output information can be applied to one or more output devices, according to methods known in the art.
  • the computer may be, for example, a personal computer, microcomputer, or workstation of conventional design.
  • Each program can be implemented in a high level procedural or object oriented programming language to communicate with a computer system. However, the programs can be implemented in assembly or machine language, if desired. The language can be a compiled or interpreted language. Each such computer program can be stored on a storage media or device (e.g., ROM or magnetic diskette or others as defined elsewhere in this disclosure) readable by a general or special purpose programmable computer, for configuring and operating the computer when the storage media or device is read by the computer to perform the procedures described herein.
  • a storage media or device e.g., ROM or magnetic diskette or others as defined elsewhere in this disclosure
  • the health-related data management system used in some aspects of the invention may also be considered to be implemented as a computer-readable storage medium, configured with a computer program, where the storage medium so configured causes a computer to operate in a specific and predefined manner to perform various functions described herein.
  • any method of nucleic acid extraction or separation from the collection solution and microorganism debris such as proteins, lipids and carbohydrates, may be performed, as would be known to one of ordinary skill in the art, including, but not limited to, the use of the standard phenol/chloroform purification, silica-based methods, and extraction methods based on magnetic glass particle.
  • compositions and methods used in the present invention are compatible with most, if not all, commercially available nucleic acid extraction compositions and methods, such as, but not limited to QiaAmp® DNA Mini kit (Qiagen®, Hilden, Germany), MagNA Pure 96 System (Roche Diagnostics, USA), and the NucIiSENS® easyMAG® extraction system (bioMerieux, France).
  • a sample enrichment step (pre-amplification) is performed.
  • the pre-amplification step can be accomplished by any methods know in the art, for example by PCR.
  • Preferable the sample enrichment step is performed using nested PCR which allows for simultaneous amplification of several target genes using multiplex PCR.
  • MDRO-associated gene are detected by any method known in the art, and preferably by multiplex real time PCR formats such as nanofluidic, microfluidic chip detection real time PCR instrumentation such as Fluidigm Biomark; bead based multiplex detection systems such as Luminex; single target or low multiplex PCR format instrumentation such as Roche Light Cycler; droplet PCR/digital PCR detection system such as Raindances's RainDrop System; or next generation sequencing technology such as Illumina MiSeq, or semiconductor sequencing such as Ion Torrent's, ion PGMTM Systeiri.
  • multiplex real time PCR formats such as nanofluidic, microfluidic chip detection real time PCR instrumentation such as Fluidigm Biomark; bead based multiplex detection systems such as Luminex; single target or low multiplex PCR format instrumentation such as Roche Light Cycler; droplet PCR/digital PCR detection system such as Raindances's RainDrop System; or next generation sequencing technology such as Illumina MiS
  • the present invention also provides for compositions and methods of detecting MDRO associated gene-specific nucleic acid sequences present in a population of polynucleotides that has been isolated or extracted from a biological sample.
  • the polynucleotide compositions of the present invention and particularly those useful in the detection of MDRO associated gene-specific nucleic acid sequences (including, for example, any one of or a combination of KPC, NDM, VIM, IMP, OXA, CTX-M or Van-A specific nucleic acids), preferably contain at least a single primer, or alternatively, two or more primers (e.g., “forward” and “reverse” primers) that may be used to facilitate amplification of the particular target nucleic acid sequence to be amplified.
  • primers e.g., “forward” and “reverse” primers
  • Exemplary primers useful in the practice of the invention include, but are in no way limited to, those primer sequences that specifically bind to the target nucleic acid sequence itself or to one or more regions immediately upstream (5′) and or downstream (3′) of the actual target nucleic sequence.
  • Primers useful in amplification of a particular sequence of interest may be designed using, for example, a computer program such as OLIGO® (Molecular Biology Insights Inc., Cascade, Colo., USA).
  • oligonucleotide primers are from about 10 to about 60 or so nucleotides in length (including, without limitation, all intermediate integers, e.g., 10, 11, 12, etc., or even 60 or more nucleotides in length), although primers of any practical length may be useful in the practice of certain embodiments of the invention.
  • the present invention provides oligonucleotide probes and primer sequences specific MDRO-associated genes.
  • exemplary oligonucleotide primer sequences are disclosed that are useful in the detection and/or amplification of nucleic acid segments that are universal across to particular types, subtypes of MGRO-associated genes.
  • the amplification and detection primers are chosen such that the primers are capable of specifically binding to most, if not, all subtypes of a particular MDRO-associated gene.
  • the primer is chosen by identifying regions of homology across the subtypes and degenerate nucleotides are utilized to accommodate for the lack of 100% homology.
  • the amplification primers and detection primers and probe bind in the same region of homology, i.e. the amplification primers and detection primers and probe are nested.
  • the primers used in the amplification step are different than the primers used in the detection step.
  • primers and probes are designed such that a single set of forward and reverse amplification primers can be used for sample enrichment and a single set of forward and reverse detection primers and probe are capable of amplifying and detecting all 15 KPC subtypes or all nine NDM subtypes.
  • primers and probes are designed such that three sets of forward and reverse amplification primers can be used for sample enrichment and three sets of forward and reverse primers and probes are capable of amplifying and detecting all 40 VIM subtypes.
  • primers and probes are designed such that five sets of forward and reverse amplification primers can be used for sample enrichment and five sets of forward and reverse primers and probes are capable of amplifying and detecting all the OXA subtypes in the OXA-51, OXA-23, OXA-48, OXA-24/40 and OXA-58 subfamilies.
  • CTX-M primers and probes are designed such that a five sets of forward and reverse amplification primers can be used for sample enrichment and five sets of forward and reverse primers are capable of amplifying and detecting all the CTX-M subtypes in the CTX-M-1, CTX-M-2, CTX-M-8, CTX-M-9 and CTX-25.
  • the primers and probes are designed such that a single set of forward and reverse amplification primers can be used for sample enrichment and a single set of forward and reverse detection primers and probe are capable of amplifying and detecting a specific group of subtypes of an MDRO-associated gene.
  • OXA primers and probes are designed such that sets of forward and reverse amplification primers can be used for sample enrichment and sets of forward and reverse primers are capable of amplifying and detecting only OXA subtypes OXA-23, 49, 73, 146, 165, 167, 168, 169, 170, 171, 225, 239
  • exemplary oligonucleotide detection probe sequences are disclosed that are particularly useful in the detection and quantitation of amplification products arising from such polynucleotides. Detection of these products when indicative of the presence of these MDRO-specific polynucleotides in a clinical sample can provide clinical diagnosticians and other medical professionals with a means for predicting and/or confirming the likelihood of a MDRO infection in patients from whom such samples are collected. Such information may also be useful in the management of care for such individuals, and may also serve as molecular markers for determining the extent, significance, and/or rate of disease progression.
  • the oligonucleotide primers and probes of the present invention are designed for the selective amplification and detection of MDRO-associated gene encoding nucleic acid segments.
  • disclosed primer sequences are suitable for use in hybridization methods, and in DNA amplification methods such as PCR-based amplification methods (including, for example, real-time PCR analyses).
  • the disclosed oligonucleotide detection probes are suitable for labeling with an appropriate label means for detection and quantitation of the products resulting from the amplification of nucleic acids using one or more pairs of the amplification primers disclosed herein.
  • oligonucleotide probes and primers finding particular utility in the practice of the disclosed methods should be of sufficient length to selectively hybridize to a complementary nucleic acid sequence, obtained from a clinical isolate of a mammalian patient that is suspected of having, or at risk for developing a MDRO infection.
  • oligonucleotide primers and probes are selected such that they selectively hybridize to specific complementary nucleic acid sequences upstream and downstream of a region of DNA that encompasses a nucleic acid sequence from an MDRO-associated gene.
  • the selection of oligonucleotide probe and primer lengths is a process well-known in the molecular biological arts, and depends upon a number of parameters.
  • the length of the selected oligonucleotide primer sequences (e.g., “forward” and “reverse” primers) and/or the length of the selected detection probe sequences (e.g., “anchor” and “sensor” probes), will likely be on the order of about 20 to 40 or so nucleotides in length, in some cases about 23 to about 40 nucleotides in length, or about 20 to about 30 nucleotides in length, although in some cases, the sizes of particular probes and primer sequences may be larger than that, and on the order of about 60 to 70 nucleotides in length.
  • the oligonucleotides selected for practice of the invention may be on the order of about 15 to 28 or so nucleotides in length or even slightly shorter, such as about 15 to about 25 nucleotides, in some embodiments.
  • oligonucleotide lengths within the various ranges stated herein are contemplated to expressly fall within the scope of the present invention.
  • oligonucleotides that are less than about 60, less than about 59, less than about 58, less than about 57, less than about 56, less than about 55, less than about 54, less than about 53, less than about 52, less than about 51, etc.
  • oligonucleotides that are less than about 50, less than about 49, less than about 48, less than about 47, less than about 46, less than about 45, less than about 44, less than about 43, less than about 42, less than about 41, as well as oligonucleotides that are less than about less than about 40, less than about 39, less than about 38, less than about 37, less than about 36, less than about 35, less than about 34, less than about 33, less than about 32, less than about 31, as well as oligonucleotides that are less than about less than about 30, less than about 29, less than about 28, less than about 27, less than about 26, less than about 25, less than about 24, less than about 23, less than about 22, less than about 21, less than about 20, less than about 19, less than about 18, less than about 17, less than about 16, less than about 15, less than about 14, and so forth.
  • nucleic acid or “polynucleotide” compositions include, but are not limited to, those that contain either single-stranded or double-stranded polynucleotides, such as for example, deoxyribonucleic acids (DNA), ribonucleic acids (RNA), peptide nucleic acids (PNA), or any combinations or derivatives thereof (including, e.g., genomic, extragenomic, plasmid, cosmid, recombinant, artificial, and/or synthetic).
  • DNA deoxyribonucleic acids
  • RNA ribonucleic acids
  • PNA peptide nucleic acids
  • Such sequences may be coding or non-coding sequences, sense, non-sense, or anti-sense sequences, and may, but need not, be present within one or more populations or pluralities of polynucleotides (either of the present invention, and a polynucleotide may, but need not, be linked to other molecules and/or support materials.
  • polynucleotides of the present invention and particularly those functioning as probes and/or primers specific for one or more particular types, subtypes, or strains of MDRO-associated genes, need not be identical, or even substantially homologous to the particular sequences employed in the various embodiments of the invention illustrated herein. While the inventors have illustrated the use of particular probe and primer sequences as tools for identifying, amplifying, and quantitating a particular MDRO-associated gene subtype or strain, such primers and/or probe sequences need not contain the particular nucleotide sequences employed in the illustrative examples provided herein.
  • polynucleotides useful as probe and/or primer sequences may include any suitable sequences that may be obtained, prepared, modified, or synthesized for such purpose.
  • the probe and primer sequences utilized specifically hybridize to their particular target sequences, and do not share significant homology or substantially bind to other viral, bacterial, or fungal species, or to the genome of the host organism from which the biological sample was originally obtained.
  • the various probes and primer compositions used for the detection of particular subtypes and/or strains of a given MDRO-associated gene also not cross-react, or hybridize to other or non-related nucleic acids that may also be present in the sample under assay.
  • the invention provides detection probes that contain at least a first sequence domain that specifically hybridizes (i.e., binds) to a suitably-detectable probe, including, without limitation, molecularly-labeled probes and derivatives thereof.
  • exemplary labeled probes are those that include radioactive, luminescent, chemiluminescent, fluorescent, enzymatic, magnetic, or spin-resonance labels known to those of ordinary skill in the molecular arts.
  • the labeled probe contains at least a first minor groove binder.
  • the detection probe may include a fluorescent label such as fluorescein, 6-carboxyfluorescein (6-FAM), or 6-carboxyfluoroscein-N-succinimidyl ester (6-FAMSE), VICTM dye and the like, or a combination thereof.
  • a fluorescent label such as fluorescein, 6-carboxyfluorescein (6-FAM), or 6-carboxyfluoroscein-N-succinimidyl ester (6-FAMSE), VICTM dye and the like, or a combination thereof.
  • the detection probes of the invention will contain at least a first sequence domain of from about 10 to about 60 nucleotides, in some instances about 10 to about 50 nucleotides, or about 10 to about 40 nucleotides, or about 10 to about 30 nucleotides, or about 10 to about 20 nucleotides in length that specifically binds to at least a first detectable probe.
  • the first sequence domain may be of any practical length within the entirety of the carrier sequence, preferably, the first sequence domain will be from about 12 to about 50 nucleotides in length; more preferably, from about 14 to about 45 nucleotides in length; still more preferably, from about 16 to about 40 or so nucleotides in length, and more preferably still, from about 18 to about 30 or so nucleotides in length.
  • probe-binding domains that are about 13 nucleotides in length, about 14 nucleotides in length, about 15 nucleotides in length, about 16 nucleotides in length, about 17 nucleotides in length, about 18 nucleotides in length, about 19 nucleotides in length, about 20 nucleotides in length, about 21 nucleotides in length, about 22 nucleotides in length, about 23 nucleotides in length, about 24 nucleotides in length, about 25 nucleotides in length, about 26 nucleotides in length, about 27 nucleotides in length, about 28 nucleotides in length, about 29 nucleotides in length, about 30 nucleotides in length, about 31 nucleotides in length, about 32 nucleotides in length, about 33 nucleotides in length,
  • the amplification primers and detection probes may be prepared by one or more suitable molecular biology techniques, including, e.g., by the in vitro transcription of a polynucleotide that includes the sequence, or alternatively, includes a nucleic acid sequence that is complementary to the sequence.
  • primers and probe are added so as to amplify and detect the desired target.
  • the composition of the invention may be formulated to contain a first pair of amplification primers that specifically bind to at least a first target region of an KPC-specific polynucleotide, and a second pair of amplification primers that specifically bind to at least a first target region of an NMM, VIM, IMP, OXA, CTX-M, Van-A, MI, SME, GIM, SPM, NMC, SFC, SHV, TEM, BEL, VEB, GES, PER, SFO, BES, TLA, ACC, CMY, MIR, ACT, DHA, MOX, FOX, or CFE-specific polynucleotide.
  • the composition when an internal positive control (IPC) is added to an initial collection solution or the extracted nucleic acid sample, the composition may be further or additionally formulated to include a first pair of amplification primers that specifically bind to at least a first target region of a particular IPC polynucleotide.
  • IPC internal positive control
  • the compositions will also further include a first detection probe that specifically binds to the amplification product produced from the first pair of amplification primers, and a second distinct detection probe that specifically binds to the amplification product produced from the second pair of amplification primers.
  • a first detection probe that specifically binds to the amplification product produced from the first pair of amplification primers
  • a second distinct detection probe that specifically binds to the amplification product produced from the second pair of amplification primers.
  • the two, three or four detection probes present in the formulation be distinct, such that each of the probes (if specifically bound to a target in the resulting amplification mixture) may be individually detectable using conventional methodologies.
  • Such probe distinctiveness is readily achievable in the conventional arts, using, for example, detection probes that include detection moieties that fluoresce at two, three or four distinctly-different wavelengths.
  • the amplification and/or detection of target nucleic acids may be done sequentially, while in other aspects, it may be desirable to amplify and/or detection multiple target nucleic acids simultaneously.
  • a given biological sample could first be screened for the presence of KPC, and if none are found, the sample then secondarily screened for the presence of NDM, VIM, IMP, OXA, CTX-M, VAN-A MI, SME, GIM, SPM, NMC, SFC, SHV, TEM, BEL, VEB, GES, PER, SFO, BES, TLA, ACC, CMY, MIR, ACT, DHA, MOX, FOX, or CFE-specific target sequence(s).
  • “moderately stringent” hybridization conditions popularized by Southern et al. are generally considered in the art to include, e.g., pre-washing in a solution containing about 5 ⁇ standard sodium citrate buffer (SSC), 0.5% sodium dodecyl sulfate (SDS), 1.0 mM ethylenediaminetetraacetic acid (EDTA) (e.g., pH 8.0); hybridizing at a temperature of from about 50° C. to about 60° C.
  • SSC standard sodium citrate buffer
  • SDS 0.5% sodium dodecyl sulfate
  • EDTA ethylenediaminetetraacetic acid
  • “stringent” hybridization conditions typically include, e.g., pre-washing in a solution containing about 5 ⁇ SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at a temperature of from about 60° C. to about 70° C. in 5 ⁇ SSC overnight; followed by washing twice at about 65 to 70° C. for 20 min with each of 2 ⁇ , 0.5 ⁇ and 0.2 ⁇ SSC containing 0.1% SDS).
  • “highly-stringent” hybridization conditions include, but are not limited to, pre-washing in a solution containing about 5 ⁇ SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at a temperature of from about 70° C. to about 75° C. in 5 ⁇ SSC overnight; followed by washing twice at about 70° C. to about 75° C. for 20 mM with each of 2 ⁇ , 0.5 ⁇ and 0.2 ⁇ SSC containing 0.1% SDS).
  • Detection probes and amplification primers may be prepared by conventional molecular biology recombination methodologies, or alternatively synthesized in whole or in part by conventional methods known in the art, including chemical synthesis (e.g., solid phase phosphoramidite chemical synthesis) and the like. Modifications in a polynucleotide sequence may also be introduced using standard mutagenesis techniques, such as oligonucleotide-directed site-specific mutagenesis. RNA molecules for use as detection probes or primers may also be directly synthesized, or alternatively, be prepared by in vitro or in vivo transcription of DNA sequences using suitable systems (such as T3, T7, and SP6 polymerases and the like).
  • suitable systems such as T3, T7, and SP6 polymerases and the like.
  • Polynucleotides of the present invention may be modified to increase stability either in vitro and/or in vivo. Such modifications include, without limitation, the addition of flanking sequences at the 5′-end, 3′-end, or both; the use of phosphorothioate or 2′-o-methyl rather than phosphodiesterase linkages in the backbone; and/or the inclusion of nontraditional bases such as inosine, queosine and wybutosine, as well as acetyl-, methyl-, thio-, or otherwise-modified forms of adenine, cytidine, guanine, thymine and uridine, or any combination thereof.
  • Nucleotide sequences as described herein may be joined or linked to a variety of other nucleotide sequences using established recombinant techniques.
  • a polynucleotide useful as an amplification probe or detection primer may be produced by cloning into any of a variety of cloning vectors, including one or more of plasmids, phagemids, lambda phage derivatives and cosmids.
  • Vectors of particular interest include expression vectors, replication vectors, probe generation vectors, and sequencing vectors.
  • a vector will contain an origin of replication functional in at least one organism, convenient restriction endonuclease sites and one or more selectable markers.
  • probe and primer-specific oligonucleotide sequences may be prepared through one or more template-dependent or amplicon-directed recombinant production methodologies that are known to those of ordinary skill in the arts.
  • the present invention provides polynucleotide compositions that may be added to the disclosed collection/storage/transport media to provide one or more amplification primer(s) and or detection probe(s) to analyze and/or characterize a population of target polynucleotides isolated, for example, from a biological sample or specimen.
  • Such polynucleotide compositions may contain one or more sequence domains to which specific polymerases may bind, and may serve as suitable amplification primers, and/or detection probes.
  • the methods of the invention are capable of detecting less than 250, 240, 230, 220, 215, 210, 200, 175, 165, 150, 100, 90, 80, 70, 60, 50, 40, 30, 20, 05 15 colony forming units per sample.
  • an “acceptable degree of diagnostic accuracy” is herein defined as a test or assay (such as the test used in some aspects of the invention for determining the clinically significant presence of DETERMINANTS, which thereby indicates the presence an infection type) in which the AUC (area under the ROC curve for the test or assay) is at least 0.60, desirably at least 0.65, more desirably at least 0.70, preferably at least 0.75, more preferably at least 0.80, and most preferably at least 0.85.
  • a “very high degree of diagnostic accuracy” it is meant a test or assay in which the AUC (area under the ROC curve for the test or assay) is at least 0.75, 0.80, desirably at least 0.85, more desirably at least 0.875, preferably at least 0.90, more preferably at least 0.925, and most preferably at least 0.95.
  • the methods predict the presence or absence of an MDRO with at least 75% total accuracy, more preferably 80%, 85%, 90%, 95%, 97%, 98%, 99% or greater total accuracy.
  • the methods predict the presence or absence of an MDRO with an MCC larger than 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8., 0.9 or 1.0.
  • the predictive value of any test depends on the sensitivity and specificity of the test, and on the prevalence of the condition in the population being tested. This notion, based on Bayes' theorem, provides that the greater the likelihood that the condition being screened for is present in an individual or in the population (pre-test probability), the greater the validity of a positive test and the greater the likelihood that the result is a true positive.
  • pre-test probability the greater the likelihood that the condition being screened for is present in an individual or in the population
  • a positive result has limited value (i.e., more likely to be a false positive).
  • a negative test result is more likely to be a false negative.
  • ROC and AUC can be misleading as to the clinical utility of a test in low disease prevalence tested populations (defined as those with less than 1% rate of occurrences (incidence) per annum, or less than 10% cumulative prevalence over a specified time horizon).
  • a health economic utility function is an yet another means of measuring the performance and clinical value of a given test, consisting of weighting the potential categorical test outcomes based on actual measures of clinical and economic value for each.
  • Health economic performance is closely related to accuracy, as a health economic utility function specifically assigns an economic value for the benefits of correct classification and the costs of misclassification of tested subjects.
  • As a performance measure it is not unusual to require a test to achieve a level of performance which results in an increase in health economic value per test (prior to testing costs) in excess of the target price of the test.
  • diagnostic accuracy In general, alternative methods of determining diagnostic accuracy are commonly used for continuous measures, when a disease category has not yet been clearly defined by the relevant medical societies and practice of medicine, where thresholds for therapeutic use are not yet established, or where there is no existing gold standard for diagnosis of the pre-disease.
  • measures of diagnostic accuracy for a calculated index are typically based on curve fit and calibration between the predicted continuous value and the actual observed values (or a historical index calculated value) and utilize measures such as R squared, Hosmer-Lemeshow P-value statistics and confidence intervals.
  • implementations of the subject matter described herein may be realized in digital electronic circuitry, integrated circuitry, specially designed ASICs (application specific integrated circuits), computer hardware, firmware, software, and/or combinations thereof.
  • ASICs application specific integrated circuits
  • These various implementations may include implementation in one or more computer programs that are executable and/or interpretable on a programmable system including at least one programmable processor, which may be special or general purpose, coupled to receive data and instructions from, and to transmit data and instructions to, a storage system, at least one input device, and at least one output device.
  • the subject matter described herein may be implemented on a computer having a display device (e.g., a CRT (cathode ray tube) or LCD (liquid crystal display) monitor) for displaying information to the user and a keyboard and a pointing device (e.g., a mouse or a trackball) by which the user may provide input to the computer.
  • a display device e.g., a CRT (cathode ray tube) or LCD (liquid crystal display) monitor
  • a keyboard and a pointing device e.g., a mouse or a trackball
  • Other kinds of devices may be used to provide for interaction with a user as well; for example, feedback provided to the user may be any form of sensory feedback (e.g., visual feedback, auditory feedback, or tactile feedback); and input from the user may be received in any form, including acoustic, speech, or tactile input.
  • the subject matter described herein may be implemented in a computing system that includes a back-end component (e.g., as a data server), or that includes a middleware component (e.g., an application server), or that includes a front-end component (e.g., a client computer having a graphical user interface or a Web browser through which a user may interact with an implementation of the subject matter described herein), or any combination of such back-end, middleware, or front-end components.
  • the components of the system may be interconnected by any form or medium of digital data communication (e.g., a communication network). Examples of communication networks include a local area network (“LAN”), a wide area network (“WAN”), and the Internet.
  • LAN local area network
  • WAN wide area network
  • the Internet the global information network
  • the computing system may include clients and servers.
  • a client and server are generally remote from each other and typically interact through a communication network.
  • the relationship of client and server arises by virtue of computer programs running on the respective computers and having a client-server relationship to each other.
  • the MDRO test uses anal swabs collected using ESwabsTM from Copan or Becton Dickinson (BD). Collected ESwabsTM should be properly labeled, stored and transported to OpGen at room temperature (20-25 C) or 4 to 8 C. ESwabsTM should be tested within 48 hours of collection.
  • primer and probe sequences useful in the methods of the invention include those listed below in Tables 2, 8 and 9. It is readily apparent to those skilled in the art that other primer and probe sequence may be utilized in practicing the claimed methods.
  • Controls for MDRO Assay are used at 3 different levels.
  • First one represents a set of controls (NEC, PEC, NTC and the Internal Amplification Control (IAC) reaction) that are required to qualify a given assay run and are defined as “Assay Run controls”. These controls are evaluated first for any given assay run and once accepted, the second level of controls (NEC, PEC, and NTC for each target) are assessed for each of the MDRO targets in the Assay run. This second level of controls qualifies a given target and is defined as “Target Controls”. Once a given target is accepted, results for each sample are evaluated against a third level that represents an Internal Amplification Control (IAC) for each and every sample to evaluate inhibition of amplification and/or detection.
  • IAC Internal Amplification Control
  • the positive extraction control monitors for any reagent failure during RT-PCR.
  • the negative extraction control detects reagent or environment contamination by any target DNA through the sample acquisition, sample DNA, extraction, and through RT-PCR.
  • the NTC detect reagents or environment contamination by any target DNA.
  • the IAC controls for specimen inhibition.
  • Each plate must contain a minimum of one specimen, one positive extraction control (PEC), one negative extraction control (NEC), and one negative template control (NTC).
  • PEC positive extraction control
  • NEC negative extraction control
  • NTC negative template control
  • sample enrichment plate containing assay reagent mix A Load 9 ⁇ l of DNA template to each well according to plate map. Load 9 ⁇ l of PEC to the PEC well(s) and load 9 ⁇ l of NEC to the NEC well(s). Load 10 ⁇ l of molecular grade water to the no template control (NTC wells(s)).
  • NTC wells(s) no template control
  • control line fluid into the accumulator 2 on the chip. Be sure to use syringes labeled 192.24 with 150 ⁇ l of control line fluid.
  • the IFC controller will display a run screen giving an estimated time of completion.
  • the methods of the present invention may include detecting MDRO-associated genes in combination with detecting a broad number of other genes that together make up the “resistome” of organisms, or the collection of antibiotic resistance in pathogenic and non-pathogenic bacteria, also referred to as The Resistome Test. See FIG. 5 and Table 1.
  • the Resistome Test can be used by a clinician to help determine which antibiotics should be used based on Resistome test result of the patient sample, either because of the presence of an individual resistance gene or a combination of resistance genes. This ability to stratify genotype is also very specific and reproducible. Organism Resistome profiles can also be matched with actual Antibiotic Susceptibility Test (AST) data. When patients with matching Resistome patterns are found their similarity or lack of similarity and antibiotic resistance can potentially be inferred from this information.
  • AST Antibiotic Susceptibility Test
  • Exemplary primer and probe sequences useful in the methods of the invention for performing The Resistome Test include those listed below in Table 10. It is readily apparent to those skilled in the art that other primer and probe sequence may be utilized in practicing the claimed methods.

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KR20170026322A (ko) 2017-03-08
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US20180342310A1 (en) 2018-11-29
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