EP1017850A2 - Genetische sequenzen, diagnoseverfahren und/ oder verfahren zur quantisierung von staphyloccoci-stämmen - Google Patents

Genetische sequenzen, diagnoseverfahren und/ oder verfahren zur quantisierung von staphyloccoci-stämmen

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Publication number
EP1017850A2
EP1017850A2 EP98944907A EP98944907A EP1017850A2 EP 1017850 A2 EP1017850 A2 EP 1017850A2 EP 98944907 A EP98944907 A EP 98944907A EP 98944907 A EP98944907 A EP 98944907A EP 1017850 A2 EP1017850 A2 EP 1017850A2
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EP
European Patent Office
Prior art keywords
nucleotide sequence
sequence
base pairs
fema
genetic
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP98944907A
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English (en)
French (fr)
Inventor
Pascal Vannuffel
Jean-Luc Gala
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Ministere de la Defense Nationale
Universite Catholique de Louvain UCL
Original Assignee
Ministere de la Defense Nationale
Universite Catholique de Louvain UCL
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Filing date
Publication date
Application filed by Ministere de la Defense Nationale, Universite Catholique de Louvain UCL filed Critical Ministere de la Defense Nationale
Priority to EP98944907A priority Critical patent/EP1017850A2/de
Publication of EP1017850A2 publication Critical patent/EP1017850A2/de
Withdrawn legal-status Critical Current

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Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/16Primer sets for multiplex assays

Definitions

  • the present: invention refers to new genetic sequences, diagnostic and/or quantification methods and devices using said sequences for the identification of various types of Staphylococci strains as well as the therapeutical aspects of said genetic sequences.
  • Methicillin-resistant coagulase-negative Staphylococci (MR-CNS) and S . aureu ⁇ (MRSA) express a high level cross -resistance to all ⁇ - lacta antibiotics (Ryffel et al . (1990), Refsahl et al . (1992)). They have an additional low-affinity penicillin- building protein, PBP2a (PBP2'), encoded by the mecA gene. The mecA determinant is found in all multiresistant staphylococcal species (Chackbart et al .
  • the femA-femB operon is one of those genetic factors essential for methicillin resistance (Berger-Bachi et al . (1989)). It is involved in the formation of the characteristic pentaglycine side chain of the SA peptidoglycan (Stranden et al . (1997)). Unlike other regulatory genes, femA was shown to retain a strong conservation over time in clinical isolates of MRSA, hence confirming its key role in cell wall metabolism and methicillin resistance (Hurlimann-Dalel et al . (1992)). In contrast to mecA, femA-femB is present both in the genome of resistant and susceptible SA strains (Unal et al . (1992), Vannuffel et al . (1995)).
  • the present invention aims to provide new genetic sequences, methods and devices for the improvement of the identification and/or the quantification of various types of Staphylococci strains through their femA-like determinants, which allow by a rapid screening their epidemiological study.
  • Another aim of the invention is to identify similar genetic sequences which may exist in known or not known Staphylococci species or other gram-positive bacterial strains .
  • a last aim of the present invention is to provide new sequences encoding femA proteins of Staphylococci species, their femA proteins, vector (s) comprising said nucleotide sequences and cell (s) transformed by said vector (s) for possible therapeutical applications .
  • the Inventors have identified new DNA and amino acid sequences from new strains of Staphylococcus hominis, Staphylococcus saprophyticus and Staphylococcus haemolyticus . Said new nucleotide sequences allow an alignment of these new sequences with the femA gene from Staphylococci previously described ( S . aureus, S . epidermidis and S. saprophyticus) .
  • the Inventors have identified for the first time a consensus femA sequence useful for molecular genotyping of different Staphylococci species which was not possible previously, when only few femA sequences of Staphylococci strains were known.
  • a first aspect of the present invention is related to the "consensus" nucleotide sequence as represented in the enclosed Figure 3.
  • the Inventors were able to provide oligonucleotides (such as primers or probes) which can be used for the genetic amplification, the identification and/or quantification of various femA sequences which are specific of known or unknown Staphylococci species.
  • the femA sequence is known to be involved with the biosynthesis of glycin-containing cross-bridges of the peptidoglycan and the peptidoglycan organisation is also known to be well conserved among various Staphylococci species and possibly among other gram-positive bacteria.
  • the new "consensus" femA sequence and said new oligonucleotides extrapolated from the alignment of the sequences presented in Figure 3, for the molecular genotyping of other Staphylococci species and possibly other gram-positive bacteria. It is also known that the femA sequence is similar to the femB sequence. Therefore, these oligonucleotides could also be used for the molecular genotyping of femB genes of different Staphylococci species or other gram-positive bacteria.
  • Another aspect of the present invention concerns the possible therapeutical uses of new femA nucleotide sequences isolated from the strains S . ho inis, S . saprophyticus, S. haemolyticus , S . lugdunensis , S. xylosus, S . capi tis, S. schleiferi and S . sciuri having a nucleotide or amino acid sequence which presents more than 85%, preferably more than 90% homology or 100% homology with the genetic sequences presented in the Figures 6 to 13, their complementary strand and functional variants thereof.
  • Functional variants of said amino acid sequences are peptides which contain one or more modifications to the primary amino acids sequence and retain the activity of the complete and wild type femA molecule.
  • Variants of the peptide are obtained by nucleotidic sequences which differ from the above-identified described sequences by a degeneration of their genetic code or are sequences which hybridise with said sequences or their complementary strand, preferably under stringent conditions such as the ones described in the document Sambrook et al . , ⁇ 9.47- 9.51 in Molecular Cloning : A Laboratory Manual , Cold Spring Harbor, Laboratory Press, Cold Spring Harbor, New York (1989) .
  • a further aspect of the present invention concerns the recombinant vector (i.e. constructions into which the sequence of the invention may be inserted for transport in different genetic environments and for expression in a host cell, s ⁇ ch as a phagemide, a virus, a plasmid, a cationic vesicle, a liposome, etc.) comprising said nucleotide sequences and their complementary strands, or the corresponding RNA sequences, possibly linked to one or more regulatory sequences or markers (resistance to antibiotics, enzyme coding sequences, ...) active into a cell.
  • a recombinant vector i.e. constructions into which the sequence of the invention may be inserted for transport in different genetic environments and for expression in a host cell, s ⁇ ch as a phagemide, a virus, a plasmid, a cationic vesicle, a liposome, etc.
  • nucleic acid sequence according to the invention may be obtained by synthetic methodology well known by the person skilled in the art, such as the one described by Brown et al .
  • recombinant host prokaryotic
  • purified proteins or peptides encoded by said nucleic acid sequences possibly linked to a carrier molecule such as BSA and obtained by said cells.
  • Said recombinant proteins or peptides could be obtained by genetic engineering or could be obtained by synthesis (see US patent 5,587,307 incorporated herein by reference) and may comprise residues enhancing their stability (resistance to hydrolysis by proteases, etc.) such as the one described by Nachman et al. (Regul .
  • a preferred vector for expression in a E. coli host cell is derived from the E. coli plasmid pET-llA available from Novagen Inc. (Catalogue No. 69436-A) .
  • the transformation technique used with the above-identified vector has been described in the US Patent 5587307.
  • a further aspect of the present invention concerns the inhibitor (used to possibly treat (with addition of antibiotics) antibiotics resistance bacteria) directed against said proteins, peptides or nucleic acid molecules.
  • said inhibitor is a antibody, preferably a monoclonal antibody, or an antisense nucleotide molecule, such as a ribozyme, which could be present in a vector in order to block the expression of said femA nucleotide sequences.
  • a last aspect of the present invention concerns the pharmaceutical composition, preferably a vaccine, against Staphylococci infections in an animal, including a human, comprising a pharmaceutically acceptable carrier and a sufficient amount of an active compound selected from the group consisting of said nucleic acid molecules, vectors, recombinant host cells transformed by said vector(s), inhibitors (directed against said proteins, peptides or nucleic acid molecules) and a mixture thereof.
  • oligonucleotides which are (DNA) sequences having between 15 and 350 base pairs, preferably between 17 and 250 base pairs (such as primers or probes) obtained from the consensus sequence of Figure 3 or its complementary strand.
  • said oligonucleotides are primers having between 15 and 45 base pairs, more preferably between 17 and 25 base pairs.
  • said oligonucleotide is a primer having between 15 and 45 base pairs, which presents more than 60%, advantageously more than 70%, preferably more than 80%, more specifically more than 90% homology with (fragments of) the "consensus" femA nucleotide sequence (CNS) identified in the Figure 3.
  • CNS "consensus" femA nucleotide sequence
  • the oligonucleotides according to the invention are new sequences or preferred fragments of known sequences of S . aureus, S. epidermidis or S . simulans but not the complete wild type known femA nucleotide sequence .
  • the oligonucleotide according to the invention is selected from the group consisting of the following nucleotide sequences :
  • AAAGACATCGACAAGCGT AAAGACATCGACAAGCGT .
  • ANCATGGNAANGAATTACCNAT and more particularly fe l (primer for the production of a probe and of marked amplicons for reverse hybridisation experiment) : GAACATGGTAATGAATTAC
  • GTTGGNGANTTNNTNAAACC and more particularly fem2 primer for the production of a probe and of marked amplicons for reverse hybridisation experiment: GTTGGTGACTTTATTAAACC
  • a further aspect of the present invention concerns the oligonucleotide being either a primer or a probe as above-described, having between 15 and 350 base pairs, preferably between 17 and 250 base pairs, or a primer having between 15 and 45 base pairs, more preferably between 17 and 25 base pairs, which will be designated hereafter as "specific primer(s)", having a nucleotide sequence which presents less than 50%, advantageously less than 40%, preferably less than 30%, more specifically less than 20% homology with (fragments of) the "consensus" femA nucleotide sequence (CNS) identified in the Figure 3 and with another femA nucleotide sequence specific for other Staphylococci strains.
  • specific primer(s) having a nucleotide sequence which presents less than 50%, advantageously less than 40%, preferably less than 30%, more specifically less than 20% homology with (fragments of) the "consensus" femA nucleotide sequence (CNS) identified in the Figure 3 and with
  • said "specific primer” is selected from the group consisting of the following nucleotide sequences :
  • oligonucleotides according to the invention are selected according to their physiochemical properties in order to avoid cross-hybridisation between themselves. Said primers are not complementary to each other and they contain a similar percentage of bases GC.
  • Said oligonucleotides are used in an identification and/or quantification method of one or more Staphylococcus species and possibly other gram-positive bacteria. Therefore, another aspect of the present invention is related to an identification and/or quantification method of a Staphylococci species which may present resistance to one or more antibiotic (s) , and is possibly combined with a method for the identification of a resistance to antibiotics, especially ⁇ -lactam antibiotics, (for instance through the identification of a variant of the mecA gene as described by Vannuffel et al . (1998)) .
  • the method for the detection, the identification and/or the quantification of a bacteria, preferably a staphylococcal species comprises the steps of : ⁇
  • a sample preferably a biological body sample obtained from a patient such as blood, serum, dialyse liquid or cerebrospinal liquid, or from any other bacteriological growth medium,
  • nucleotide sequence with one or more universal oligonucleotide (s) (universal primer (s) ) according to the invention, and
  • oligonucleotide (s) preferably immobilised on a solid support.
  • the comparative measure of the length of a possibly amplified nucleotide sequences can be performed by the analysis of their migration (compared with a known ladder) upon an electrophoresis gel .
  • the genetic amplification technique is selected from the group consisting of PCR (US patent 4,965,188), LCR (Landgren et al . , Sciences, 241, pp.
  • the specific detection of the possibly amplified nucleotide sequences can be obtained by the person skilled in the art by using known specific gel electrophoresis techniques, in situ hybridisation, hybridisation on solid support, in solution, on dot blot, by Northern blot or Southern blot hybridisation, etc.
  • the probes which are specific of the bacteria are immobilised on a solid support according to the method described in the international patent application W098/11253 incorporated herein by reference.
  • Said specific oligonucleotides have a length comprised between 50 and 350 base pairs, preferably between 120 and 250 base pairs, and are fixed to the solid support by a terminal 5 ' phosphate upon an amine function of the solid support by carbodiimide reaction (as described in the document W098/11253 incorporated herein by reference) .
  • the solid support can be selected from the group consisting of cellulose or nylon filters, plastic supports such as 96-well microtiter plates, microbeads, preferably magnetic microbeads, or any other support suitable for the fixation of a nucleotide sequence.
  • the method according to the invention can be advantageously combined with another specific detection step of a possible resistance to antibiotics, especially ⁇ -lactam antibiotics (for instance through the identification by the above-described technique of variants of the mecA gene as described by Vannuffel et al . (1998)) .
  • the present invention concerns also a diagnostic and/or quantification device or kit for the identification and/or the quantification of a Staphylococcus species or other gram-positive bacteria, comprising the oligonucleotides according to the invention and possibly all the media necessary for the identification of a (possibly amplified) nucleotide sequence of said bacteria through any one of the above-described methods.
  • the method and device according to the invention are adapted for the quantification of said Staphylococci strains by the use of a "internal or external standard sequence", preferably the one described in the patent application W098/11253 incorporated herein by reference .
  • the nucleic acid sequence from a Staphylococcus species is amplified by a "universal primer” and by a "specific primer” which is specific for S. aureus .
  • the identification of S . aureus will be obtained upon an agarose electrophoresis gel wherein the amplified nucleotide sequence (shorter than the amplified nucleotide sequence of another Staphylococci species such as S . epidermidis) and identified by the use of a comparative ladder.
  • a Staphylococcus species (such as S . aureus) is identified by reverse hybridisation of the amplified nucleotide sequence with a probe which is specific of said bacteria and which is immobilised on a solid support such as filter.
  • the Figure 1 represents 5 partially overlapping fragments of the femA genes from S . hominis,
  • the Figure 2 represents the alignment of the nucleotide sequences of femA genes from S. hominis
  • the Figure 3 represents the consensus sequence according to the invention.
  • the Figure 4 represents the result of differential diagnosis between different strains of
  • FIG. 5 represents amplification of CNS species under universal conditions.
  • Figures 6 to 13 represent the complete femA wild type genetic sequence of the strains S . hominis,
  • Fragments of the femA genes from S. hominis and S. saprophyticus have been obtained by PCR amplification, in low stringency annealing conditions. Primers used for amplification are matching the potentially conserved regions and have been designed according to sequences homologies between S. aureus, S . sapropyticus and S . epidermidis femA nucleotide sequences. For both S. hominis and S . saprophyticus species, 5 partially overlapping fragments have been synthesised allowing the sequencing of the entire femA genes (Fig. 1) .
  • Example 2 Identification of a consensus sequence Alignment of the nucleotide sequences of femA genes from S. hominis and S . saprophyticus as well as with femA genes sequenced to date from S . aureus (GenBank accession number M23918) , S. epidermidis (GenBank accession number U23713) and S . haemolyticus is presented in Fig. 3 and has allowed to propose a "consensus" femA nucleotide sequence (CNS) whose genomic organisation displays highly conserved regions flanked by variable ones. On this basis, interspecies phylogenetic variations could be exploited to design genotyping strategies for species-specific identification of Staphylococci .
  • the "consensus” sequence is therefore a powerful molecular tool for specific diagnostic of staphylococcal infections.
  • Example 3 Sequencing of other staphylococcal femA genes The consensus sequence can be exploited for designing universal primers allowing the production, under permissive annealing conditions, of overlapping PCR products whose sequencing will identify the entire femA sequence .
  • Example 4 Differential diagnosis between S . aureus . S . epidermidis , S. hominis and S . saprophyticus by reverse hybridisation
  • the Inventors have set up a reverse hybridisation assay for rapid and combined identification of the most clinically relevant Staphylococci species, and their mecA status.
  • Two set j S of primers chosen in a conserved domain of the consensus sequence (bioUl-bioU3 and feml- fem3bio) , amplifying a 286 and bio-220 bp fragments, respectively) were synthesised.
  • Species-specificity of femA amplicons was insured by the genomic variability between the conserved regions.
  • FemA probes were immobilised on nylon strips. Hybridisation was performed with biotinylated femA PCR fragments from the strain of interest .
  • the strategy was first assessed with ATCC strains ⁇ S . aureus, S . epidermidis, S . hominis and S . saprophyticus) (Fig. 4) . Specificity was identified by standard methods. Accuracy was 100% for species identification.
  • Example 5 Differential diagnosis between staphylococcal species This assay is able to identify any staphylococcal species if following requirements are fulfilled :
  • primers feml , fem2 and fem3bio are universal for Staphylococci ; - there is a wide enough phylogenetic variation between any CNS species to promote a specific hybridisation.
  • the first requirement is fulfilled for, i.e., S . haemolyticus, S. capi tis, S. cohnii , S. xylosus, S. simulans, S. lugdunensis, ⁇ . schleiferi and ⁇ . warneri strains (Fig. 5) .
  • Example s Multiplex—amplification __£ femA and m r.A genetic determinants £Q£ a molecular diagnosis of a apar;. fin staphylococcal infection
  • ETA Endotracheal aspirates
  • Clinical specimens were homogenised in 5 ml of TE buffer (20 mM TRIS HCl, pH 8.0 , 10 mM EDTA) containing 2% (w/v) SDS.
  • the homogenate (1.5 ml) was then centrifuged for 5 minutes at 7500 xg.
  • the cellular pellet was washed once with TE buffer lysed in the presence of 1% (v/v) Triton X-100 and 50 ⁇ g of lysostaphin (Sigma) and incubated for 15 minutes at 37 °C. Lysis was completed by adding 100 ⁇ g of proteinase K (Boehringer) .
  • the lysate was incubated for another 5 minutes at 55 °C and 5 minutes at 95 °C, and centrifuged at 4000 xg for 5 minutes.
  • Staphylococci in ETA was completed in less than 6 hours either on the day of the samples' collection. This is an advantage with respect to the time required to conventional identification and susceptibility tests (48 to 72 hours) .
  • Two primers were selected among the conserved parts of the consensus sequence for the amplification of the femA gene.
  • primers are femSl , femS2 and femASl (anti-sense primer) .
  • ADN from strains of Staphylococcus hominis, saprophyticus, haemolyticus, lugdunensis, schleiferi , sciuri , xylosus, simulans, capi tis, gallinaru , cohnii and wameri were amplified from said primers and amplification fragments were cloned in the vector pCR ® - XLTOPO and introduced by electroporation in E. coli cells TOP10 (TOPO XL PCR Cloning Kit ® , Invitrogen, Carlsbad, CA) .
  • Taq Dye Deoxy Terminator Cycle ® sequencing on a ABI 277 DNA sequencer ® PE Applied Biosystems, Foster City, CA
  • primers femSl or femS2 or femASl fsqlS and fsqlAS fsq2S and fsq2AS fsq3S and fsq3AS fsq4S and fsq4AS fsqBS and fsq ⁇ AS fsq ⁇ S and fsq ⁇ AS

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EP98944907A 1997-09-26 1998-09-28 Genetische sequenzen, diagnoseverfahren und/ oder verfahren zur quantisierung von staphyloccoci-stämmen Withdrawn EP1017850A2 (de)

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EP98944907A EP1017850A2 (de) 1997-09-26 1998-09-28 Genetische sequenzen, diagnoseverfahren und/ oder verfahren zur quantisierung von staphyloccoci-stämmen

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EP97870146 1997-09-26
EP97870146 1997-09-26
EP98944907A EP1017850A2 (de) 1997-09-26 1998-09-28 Genetische sequenzen, diagnoseverfahren und/ oder verfahren zur quantisierung von staphyloccoci-stämmen
PCT/BE1998/000141 WO1999016780A2 (en) 1997-09-26 1998-09-28 Genetic sequences, diagnostic and/or quantification methods for the identification of staphylococci strains

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EP1096024A1 (de) * 1999-10-28 2001-05-02 Remacle, José Verfahren und Reagentiensatz zum Auswählen und/oder Quantifizieren von multiplen homologen Nukleinsäuresequenzen unter Verwendung von Sondenanordnungen
US7875442B2 (en) 2000-03-24 2011-01-25 Eppendorf Array Technologies Identification and quantification of a plurality of biological (micro)organisms or their components
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US7202026B2 (en) * 2000-03-24 2007-04-10 Eppendorf Array Technologies Sa (Eat) Identification of a large number of biological (micro)organisms groups at different levels by their detection on a same array
EP1136566A1 (de) * 2000-03-24 2001-09-26 Facultés Universitaires Notre-Dame de la Paix Methode und Kit zum Nachweis und/oder Quantifizierung von homologen Sequenzen mittels Arrays
US7829313B2 (en) 2000-03-24 2010-11-09 Eppendorf Array Technologies Identification and quantification of a plurality of biological (micro)organisms or their components
US7090997B2 (en) * 2000-10-26 2006-08-15 Eisai Co., Ltd. Diagnostic agent and test method for colon cancer using tannase as index
US7666588B2 (en) 2001-03-02 2010-02-23 Ibis Biosciences, Inc. Methods for rapid forensic analysis of mitochondrial DNA and characterization of mitochondrial DNA heteroplasmy
AU2013231102B2 (en) * 2001-03-02 2016-04-28 Ibis Biosciences, Inc. Methods for rapid identification of pathogens in humans and animals
WO2002082086A2 (en) * 2001-03-15 2002-10-17 Jacques Schrenzel Detection of methicillin-resistant staphylococcus aureus (mrsa)
JP2006516193A (ja) 2002-12-06 2006-06-29 アイシス・ファーマシューティカルス・インコーポレーテッド ヒトおよび動物における病原体の迅速な同定方法
WO2005017202A2 (en) 2003-05-13 2005-02-24 Gen-Probe Incorporated Method and kit for identifying antibiotic-resistant microorganisms
US7338763B2 (en) 2004-06-02 2008-03-04 Eppendorf Array Technologies S.A. Method and kit for the detection and/or quantification of homologous nucleotide sequences on arrays
KR20200046106A (ko) * 2017-10-12 2020-05-06 미쓰이 가가쿠 가부시키가이샤 mecA 유전자 증폭용 프라이머 페어, mecA 유전자 검출 키트 및 mecA 유전자 검출 방법
CN112195225A (zh) * 2020-10-14 2021-01-08 南通大学附属医院 基于耐药基因MecA检测耐甲氧西林葡萄球菌的方法
WO2022253741A1 (en) 2021-06-02 2022-12-08 Syngulon S.A. Cerein 7b bacteriocin for new application
US20240285726A1 (en) 2021-06-02 2024-08-29 Syngulon S.A. Bacteriocin for new application

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