Rapid method for detection of methicillin-resistant staphylococci

Abstract: The present invention provides a method for the detection of methicillin-resistant staphylococci using the polymerase chain reaction. The reaction detects the presence of the mecA gene, which encodes penicillin binding protein 2A. Also provided is a method for the rapid release of DNA from staphylococci. The two methods can be used in combination for a rapid and sensitive route to the detection of these dangerous pathogens.

Description: Methicillin resistance in staphylococci is an important unversal problem in hospitals and geriatric care centers. Both methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant Staphylococcus epidermis (MRSE) are common nosocomial pathogens. The infections they cause are serious and difficult to treat. Horan et al ., Morbid Mortal . Weekly Rep . 35 :1755 (1984); Maple et al ., Lancet i :537 (1989). Only a few antibiotics are available for treatment and they all have undesirable side effects. Hackbarth and Chambers, Antimicrob . Agents Chemother . 33 :995 (1989). Currently, time-consuming, labor intensive, and somewhat unreliable methods are employed for the detection of MRSA/MRSE. Id These methods include disk diffusion, broth dilution and agar screening. Id Such methods do not reliably detect heterogeneously resistant staphylococci. Thus, it is imperative to develop a rapid, standardized, accurate and sensitive method for the detection of methicillin resistance in staphylococci. MRSA/MRSE carry the mecA gene which encodes penicillin binding protein 2a (PBP2a). This proteins responsible for the phenotypic expression of methicillin resistance in staphylococci. Chambers, Antimicrob . Agents Chemother . 33 :424 (1989); Hackbarth and Chambers, Antimicrob . Agents Chemother . 33 :991 (1989); Tonin and Tomasz, Antimicrob . Agents . Chemother . 30 :577 (1986). Staphylococcal strains susceptible to methicillin do not harbor a mecA gene. Therefore, the mecA , gene is a useful molecular handle for rapid identification of MRSA/MRSE. Detection of mecA by DNA hybridization has provided a relatively sensitive method for identifying MRSA/MRSE strains. Archer and Penell, Antimicrob . Agents Chemother . 34 :1720 (1990); Lencastre et al ,. Antimicrob . Agents Chemother . 35 :575 (1991). However, DNA hybridization suffers from several disadvantages. A large number of cells are required, DNA extraction and immobilization on a membrane is a time-consuming process, and frequently radioactive isotopes are employed, although recently non-radioactive probes have become available. Ligozzi et al ., Antimicrob . Agents Chemother . 35 :575 (1991). The present invention provides a method for detecting methicillin-resistant staphylococcal infections, said method comprising: a) performing the polymerase chain reaction on clinical samples suspected of staphylococcal infection, said polymerase chain reaction being primed by DNA primers composed of two oligonucleotides of high G+C content, wherein one oligonucleotide has a DNA sequence comprised by the coding strand of a Staphylococcus mecA gene and the second DNA primer has a DNA sequence comprised by the non-coding strand of a Staphylococcus mecA gene; and b) analyzing the reaction product of step a. The present invention also provides a method for the rapid release of DNA from staphylococci, said method comprising: a) treating a sample containing staphylococci with lysostaphin; b) treating the resultant sample of step a with proteinase K; and c) incubating the resultant sample of step b in a boiling water bath. Additionally, the present invention provides a method for detecting methicillin-resistant staphylococcal infections in a sample of interest, said method comprising: a) treating a sample of interest with lysostaphin; b) treating the resultant sample of step a with proteinase K; c) incubating the resultant sample of step b in a boiling water bath; d) performing the polymerase chain reaction on the resultant sample of step c, said polymerase chain reaction being primed by DNA primers, said DNA primers being composed of two oligonucleotides of high G+C content, wherein one oligonucleotide has a DNA sequence comprised by the coding strand of a Staphylococcus mecA gene and the second DNA primer has a DNA sequence comprised by the non-coding strand of a Staphylococcus mecA gene; and e) analyzing the reaction product of step d. For purposes of the present invention the following terms are defined below: High G+C content - G+C content significantly higher than the average 30.5% G+C content of staphylococcal mecA genes. mecA gene - a gene encoding penicillin binding protein 2A, which is responsible for methicillin resistance. Methicillin-resistant staphylococci - staphylococci which are resistant to all beta-lactams, including cephalosporins and penicillin derivatives such as methicillin and oxacillin. PBP2A - penicillin binding protein 2A. The present invention provides a method for detecting methicillin-resistant staphylococcal infections, said method comprising: a) performing the polymerase chain reaction on clinical samples suspected of staphylococcal infection, said polymerase chain reaction being primed by DNA primers, said DNA primers being composed of two oligonucleotides of high G+C content, wherein one oligonucleotide has a DNA sequence comprised by the coding strand of a Staphylococcus mecA gene and the second DNA primer has a DNA sequence comprised by the non-coding strand of a Staphylococcus mecA gene; and b) analyzing the reaction product of step a. The polymerase chain reaction (PCR) is now well-known in the art as a route to the amplification of minute quantities of DNA. See U.S. Patents 4,683,195, 4,800,159 and 4, 683,202. The technique has been applied in clinical settings to the detection of a variety of different pathogens. See. e.g. , Cassol et al ., J . Clin . Microbiol . 29 :667-671 (1991); Lopez et al ., J . Clin . Microbiol . 29 :578-582 (1991); Brisson-Noel et al ., Lancet ii :1069-1071 (1989); Valentine et al ., J . Clin . Microbiol . 29 :689-695 (1991); and Gouvea et al ., J . Clin . Microbiol . 29 :529-523 (1991). The technique has been used to detect toxins of Staphylococcus aureus but until the present invention the technique was not applied to the detection methicillin-resistant staphylococci. Staphylococci resistant to beta-lactams, particularly Staphylococcus aureus and Staphylococcus epidermidis , represent a significant and steadily increasing problem for physicians. Due to the speed with which these bacteria can cause death, it is advantageous to quickly ascertain whether the organisms present in a patient are non-responsive to betalactams. The present invention provides a method which can be performed significantly faster than prior art methods (Hackbarth and Chambers, Antimicrob . Agents and Chemother . 33 :995-999 (1989)), including methods based on DNA hybridization (Ligozzi et al ., Antimicrob . Agents and Chemother . 35 :575-578 (1991) and Archer and Pennel, Antimicrob . Agents and Chemother . 34 :1720-1724 (1990)). The extreme sensitivity afforded by the PCR is another vital aspect of the present invention. The methicillin-resistant staphylococci are open heterogeneously resistant. Thus, non-DNA based resistance determinations can give inconsistent results. Penicillin binding protein 2A confers methicillin resistance by having a low affinity for the beta-lactams. The proteins encoded by the mecA gene. The present invention will enable the detection of any staphylococci bearing the mecA gene. The clinically relevant staphylococcal strains are primarily S . epidermidis and S . aureus and, occasionally, S . haemolyticus . Rarely problematic strains are S . simulans , S . carnosus and S . saprophyticus . All the mecA genes which have been isolated and sequenced have a very high similarity (>99%), thus allowing the use of one or two sets of primers to detect all mecA -containing strains. If primers are made from regions of the gene which are known to contain variance among mecA genes isolated from different sources, the length of the primers used should be at least thirty nucleotides to ensure specific priming. These regions correlate to nucleotides 605-607, 615-617, 697-699, 746-747, 841, 1010-1011, 1819, and 1933 of SEQ ID NO:1. The average G+C content of the known mecA genes is about 30.5%. To ensure specific priming, the G+C content of the DNA primers used for the PCR should be significantly higher than 30.5%, preferably about 50% or higher. The sequences of the DNA primers may be derived from any mecA gene. The sequences of some of these genes can be found in Song et al ., FEBS Letters 221 :167-171 (1987) ( S . aureus TK784) and Ryffel et al ., Gene 94 :137-38 (1990) ( S . aureus BB270 and S . epidermidis WT55). Additionally, the DNA primers may be derived from the S . aureus 27R mecA gene, set out as SEQ ID NO:1. Skilled artisans will recognize that, within a particular set of primers, one of the oligonucleotides should be derived from the coding strand of the gene and the other oligonucleotide should be derived from the non-coding strand. Preferred DNA primers have sequences corresponding to nucleotides 141-160 of SEQ ID NO:1 and the inverse complement of nucleotides 1929-1952 of SEQ ID NO:1. The primers can be synthesized by the modified phosphotriester method using fully protected deoxyribonucleotide building blocks. Such synthetic methods are well known in the art and can be carried out in substantial accordance with Itakura et al ., Science 198 :1056 (1977), Crea et al ., Proc . Nat'l Acad . Sci . USA 75 :5765 (1978), Hsiung et al ., Nuc . Acids Res . 11 :3227 (1983) or Narang et al ., Methods in Enzymology 68:90 (1980). An especially preferred method employs automated DNA synthesizers such as the Applied Biosystems 380B DNA synthesizer (850 Lincoln Centre Drive, Foster City, CA 94404). Protocols for performing the PCR reaction are set out in PCR Protocols: A Guide to Methods and Applications , ed. Michael A. Innis et al ., Academic Press, Inc., 1990. An especially preferred protocol is described in the Examples herein. The results of the reaction may be analyzed in any way desired; a preferred method is by agarose gel electrophoresis. It may be desirable to further confirm the presence of staphylococci comprising the mecA gene by performing "nested PCR." In this technique, two consecutive PCRs are performed. The oligonucleotides used to prime the second PCR should be derived from DNA sequences of the mecA gene interior to the DNA sequences on which the first set of primers are based. Preferred DNA primers for the second PCR have sequences corresponding to nucleotides 568-593 of SEQ ID NO:1 and the inverse complement of nucleotides 1647-1670 of SEQ ID NO:1. The present invention also provides a method for the rapid release of DNA from staphylococci, said method comprising: a) treating a sample containing staphylococci with lysostaphin; b) treating the resultant sample of step a with proteinase K; and c) incubating the resultant sample of step b in a boiling water bath. The method of the present invention is much faster than prior art staphylococcal DNA extraction methods. A preferred embodiment of the rapid release method is outlined in the Examples. The method is particularly useful in combination with the methicillin-resistant staphylococci detection technique of the present invention. Thus, the present invention also provides a method for detecting methicillin-resistant staphylococcal infections in a sample of interest, said method comprising: a) treating a sample interest with lysostaphin; b) treating the resultant sample of step a with proteinase K; c) incubating the resultant sample of step b in a boiling water bath; d) performing the polymerase chain reaction on the resultant sample of step c) said polymerase chain reaction being primed by DNA primers, said DNA primers being composed of two oligonucleotides of high G+C content, wherein one oligonucleotide has a DNA sequence comprised by the coding strand of a Staphylococcus mecA gene and the second DNA primer has a DNA sequence comprised by the non-coding strand of a Staphylococcus mecA gene; and e) analyzing the reaction product of step d. This method represents a combination of the rapid release DNA extraction method and the method for detecting methicillin-resistant staphylococci outlined above. The various considerations discussed regarding those two techniques are equally applicable when the methods are used in combination. The detection of methicillin-resistant staphylococci via the present invention requires only three hours. In contrast, when the prior art DNA extraction method is used in lieu of the rapid release DNA extraction method, six hours are required. Any additional time is significant in potential life or death situations such as methicillin-resistant staphylococcal infections. The speed and sensitivity of the present invention allows one to avoid empirical antibiotic therapy, which is fraught with liabilities such as high cost, toxicity factors and resistance development. The present invention may be used to detect methicillin-resistant staphylococci in any internal body fluid, including blood, urine, spinal fluid and fluid drained from an abscess. If desired, the samples may be cultured and the PCR performed on a sample of the bacteria from the growth medium. The use of the PCR on body fluids is known in the prior art. See , e.g. , Cassol et al ., J . Clin . Microbiol . 29 :667-671 (1991); Lopez et al ., J . Clin . Microbiol . 29 :578-582 (1991); and Brisson-Noel et al ., Lancet ii :1069-1071 (1989). The following Examples are intended to further illustrate and exemplify, but not limit the scope of, the present invention. Example 1 A total of 70 staphylococcal strains (33 S . aureus and 37 S . epidermidis ) isolated from various clinical settings were examined. Species identification was done with a Staph-Ident™ Diagnostic Kit (Analytab, Sherwood Medical, Plainview, NY). To verify the results obtained with the PCR, all were screened for methicillin resistance by growth on Mueller-Hinton agar (Difco, Detroit, Ml) supplemented with 4% sodium chloride and 6 µg oxacillin/ml. Inoculated plates were incubated for 24 hours at 35 °C and examined for the presence of growth. Sixteen of 33 S . aureus and 27 of 37 S . epidermidis were categorized as methicillin-resistant using this method. Example 2 Each strain examined for methicillin resistance in Example 1, above, was treated as follows. Bacteria were harvested from either TY agar plates (one loopful) or TY broth cultures (one ml of overnight culture diluted to 10 8 bacteria/ml). Cells from broth medium were harvested by centrifugation for 30 seconds in a microcentrifuge. Cells from either source were resuspended in 50 µl of lysostaphin solution (100 µg/ml in water, Sigma Chemical Co., St. Louis, MO). Cell suspensions were incubated at 37 °C. After 10 minutes, 50 µl proteinase K solution (100 µg/ml in water, Sigma), and 150 µl of 0.1 M Tris, pH 7.5, were added. The cell suspensions were incubated at 37 °C for an additional 20 minutes and then placed in a boiling water bath for 10 minutes. This treatment effectively lysed S . aureus or S . epidermidis cells and prevented DNase activity. Ten µl from these cell lysates were used directly in PCRs. Example 3 Two primers were chosen for the PCR that were separated by 1.8 kb in the mecA open reading frame. The sequences of the two primers were 5′-GTTGTAGTTGTCGGGTTTGG-3′(nucleotides 141-160 of SEQ ID NO:1) and 5′-CCACCCAATTTGTCTGCCAGTTTCTCC-3′(inverse complement of nucleotides 1929-1952 of SEQ ID NO:1). The PCR was performed in a DNA Thermal Cycler using a Gene Amp Kit according to the manufacturer's instructions (Perkin Elmer Cetus, Norwalk, CT). A thermal step program that included the following parameters was used for DNA amplification: denaturation at 94 °C for 30 seconds, annealing at 55 °C for 30 seconds, primer extension at 72 °C for two minutes, for a total of 30 cycles. Ten µl of the PCR solution were analyzed by electrophoresis on a 0.8% agarose gel. A positive result was indicated by the presence of a 1.8 kb amplified DNA fragment. In all, 69 of the 70 staphylococcal strains produced exactly the same result with PCR and the oxacillin susceptibility test. Examination of the single exception revealed that it was a mixed culture containng a rapidly growing methicillin-sensitive strain ( mecA -) and a slower growing methicillin-resistant ( mecA + ) strain. When the strains were separated the susceptibility test and the PCR were in agreement. Subsequent nested PCR analysis of the intial DNA sample with the internal DNA primers (corresponding to nucleotides 568-593 of SEQ ID NO:1 and the inverse complement of nucleotides 1647-1670 of SEQ ID NO:1) produced a positive PCR result. No isolates were found to be mecA sensitive but methicillin resistant. These results emphasize the fact that a positive result in a DNA-based test correlates very well with the methicillin-resistant phenotype. SEQUENCE LISTING (1) GENERAL INFORMATION: (i) APPLICANT: Eli Lilly and Company (ii) TITLE OF INVENTION: Rapid Method for Detection of Methicillin Resistant Staphylococci (iii) NUMBER OF SEQUENCES: 2 (iv) CORRESPONDENCE ADDRESS: (A) ADDRESSEE: C. M. Hudson (B) STREET: Erl Wood Manor (C) CITY: Windlesham (D) STATE: Surrey (E) COUNTRY: United Kingdom (F) ZIP: GU20 6PH (v) ATTORNEY/AGENT INFORMATION: (A) NAME: C. M. Hudson (B) REGISTRATION NUMBER: 307 (C) REFERENCE/DOCKET NUMBER: X-8573 (vi) TELECOMMUNICATION INFORMATION: (A) TELEPHONE: 0276 78441 (B) TELEFAX: 0276 78306 (2) INFORMATION FOR SEQ ID NO:1: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 2111 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: both (D) TOPOLOGY: linear (ii) MOLECULE TYPE: DNA (genomic) (iii) HYPOTHETICAL : NO (iv) ANTI-SENSE: NO (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: 105..2111 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:1: (2) INFORMATION FOR SEQ ID NO:2: (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 668 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:

Claims: A method for detecting methicillin resistant staphylococcal infections, said method comprising: a) performing the polymerase chain reaction on clinical samples suspected of staphylococcal infection, said polymerase chain reaction being primed by DNA primers, said DNA primers being composed of two oligonucleotides of high GC content, wherein one oligonucleotide has a DNA sequence comprised by the coding strand of a Staphylococcus mecA gene and the second DNA primer has a DNA sequence comprised by the non-coding strand of a Staphylococcus mecA gene; and b) analyzing the reaction product of step a. The method of Claim 1 wherein the GC content of the DNA primers is approximately 50% or greater. The method of Claim 2 wherein the sequences of the DNA primers are nucleotides 141-160 of SEQ ID NO:1 and the inverse complement of nucleotides 1929-1952 of SEQ ID NO:1. The method of Claim 1 wherein an additional subsequent polymerase chain reaction is performed using DNA primers interior to the DNA primers used in the initial polymerase chain reaction. The method of Claim 4 wherein the sequences of the interior DNA primers are nucleotides 568-593 of SEQ ID NO:1 and the inverse complement of nucleotides 1647-1670 of SEQ ID NO:1. The method of Claim 1 wherein the sequence of the DNA primers is comprised by the coding and non-coding strands of a gene selected from a group consisting of Staphylococcus aureus and Staphylococcus epidermidis mecA genes. The method of Claim 6 wherein the gene is selected from a group consisting of the S . aureus 27R, S . aureus BB270, S . aureus TK784, and the S. epidermidis WT55 mecA genes. The method of Claim 1 wherein the method is used to detect methicillin resistant staphylococci selected from the group consisting of S . aureus , S . epidermidis , S . haemolyticus , S . simulans , S . carnosus , and S . saprophyticus . The method of Claim 1 wherein the reaction product of step a) is analyzed by gel electrophoresis. A method for the rapid release of DNA from staphylococci, said method comprising: a) treating a sample containing staphylococci with lysostaphin; b) treating the resultant sample of step a with proteinase K; and c) incubating the resultant sample of the step in a boiling water bath. The method of Claim 10 wherein the sample containing staphylococci is derived from blood, urine, spinal fluid, an abscess or bacteriological growth medium. A method for detecting methicillin resistant staphylococcal infections in a sample of interest, said method comprising: a) treating a sample of interest with lysostaphin; b) treating the resultant sample of step a with proteinase K; c) incubating the resultant sample of step b in a boiling water bath; d) performing the polymerase chain reaction on the resultant sample of step c) said polymerase chain reaction being primed by DNA primers, said DNA primers being composed of two oligonucleotides of high GC content, wherein one oligonucleotide has a DNA sequence comprised by the coding strand of a Staphylococcus mecA gene and the second DNA primer has a DNA sequence comprised by the non-coding strand of a Staphylococcus mecA gene; and e) analyzing the reaction product of step d. The method of Claim 12 wherein the GC content of the DNA primers is approximately 50% or greater. The method of Claim 13 wherein the sequences of the DNA primers are nucleotides 141-160 of SEQ ID NO:1 and the inverse complement of nucleotides 1929-1952 of SEQ ID NO:1. The method of Claim 14 wherein an additional subsequent polymerase chain reaction is performed using DNA primers interior to the DNA primers used in the initial polymerase chain reaction. The method of Claim 15 wherein the sequences of the interior DNA primers are nucleotides 568-593 of SEQ ID NO:1 and the inverse complement of nucleotides 1647-1670 of SEQ ID NO:1 The method of Claim 12 wherein the sequence of the DNA primers is comprised by the coding and non-coding strands of a gene selected from a group consisting of Staphylococcus aureus and Staphylococcus epidermidis mecA genes. The method of Claim 17 wherein the sequence of the DNA primers is comprised by the coding and non-coding stands of a gene selected from a group consisting of the S . aureus 27R, S . aureus BB270, S . aureus TK784, and the S . epidermis WT55 mecA genes. The method of Claim 12 wherein the method is used to detect methicilin-resistant staphylococci selected from the group consisting of S . aureus , S . epidermidis , S . haemolyticus , S . simulans , S . carnosus , and S . saprophyticus . The method of Claim 12 wherein the reaction product of step d) is analyzed by gel electrophoresis. The method of Claim 12 wherein the sample of interest is derived from blood, urine, spinal fluid, an abscess or bacteriological growth medium.

Inventors: SKATRUD PAUL LUTHER, UNAL SERHAT, SKATRUD, PAUL LUTHER, UNAL, SERHAT
Applicants: LILLY CO ELI, ELI LILLY AND COMPANY
Application year: 1992
Main classification: C12Q1
IPC codes: C12R1, C12Q1, C12N15