Depolymerase Dep_G_1 of an escherichia coli bacteriophage and use thereof
Patent Information
- Application Number
- CN202610497479.7
- Authority / Receiving Office
- CN · China
- Patent Type
- Applications(China)
- Current Assignee / Owner
- Filing Date
- 2026-04-15
- Publication Date
- 2026-10-09
AI Technical Summary
然而,针对当前临床流行的耐药多耐药大肠杆菌菌株,具有高效裂解活性的新型解聚酶仍有待发现
本发明首次从噬菌体vB_Eco_G1中鉴定并表达得到解聚酶Dep_G_1,解聚酶Dep_G_1 对多耐药大肠杆菌能形成清晰的抑菌斑,具有直接的体外裂解活性,该解聚酶可用于开发针对多耐药大肠杆菌的抗菌蛋白制剂,可用于清除物体表面多耐药大肠杆菌污染的清洁剂或消毒剂的制备中。
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Abstract
Description
Technical Field
[0001] This invention belongs to the field of biotechnology, specifically relating to a depolymerase Dep_G_1 of Escherichia coli bacteriophage and its application. Background Technology
[0002] Escherichia coli is a common opportunistic pathogen in clinical practice, causing various diseases such as urinary tract infections and sepsis. With the overuse of antibiotics, multidrug-resistant Escherichia coli (MDR-E. coli), especially strains producing extended-spectrum β-lactamases (ESBLs) and carbapenemases (such as NDM-1), are prevalent worldwide, leading to clinical treatment failures and increased mortality rates, necessitating the development of novel antibacterial agents.
[0003] Phage depolymerases are tail-associated depolymerases encoded by bacteriophages that specifically degrade capsular polysaccharides, lipopolysaccharides, or peptidoglycans in the bacterial cell wall, leading to bacterial lysis. Compared to intact bacteriophages, recombinant depolymerases have advantages such as standardized production, lack of bacterial toxin genes, and non-self-replication, making them a highly promising new type of antimicrobial protein.
[0004] Currently, several phage depolymerases targeting *E. coli* have been reported, and some of the disclosed depolymerases can effectively lyse specific serotypes of *E. coli*. However, novel depolymerases with highly efficient lytic activity against currently prevalent drug-resistant and multidrug-resistant *E. coli* strains remain to be discovered. Therefore, developing new phage depolymerases that can effectively target multidrug-resistant *E. coli* is of great significance. Summary of the Invention
[0005] To overcome the technical problems existing in the background art, the present invention proposes a depolymerase Dep_G_1 of Escherichia coli bacteriophage and its application. The depolymerase Dep_G_1 isolated and purified by the present invention can effectively lyse multidrug-resistant Escherichia coli and has good application prospects in the preparation of preparations for inhibiting or lysing multidrug-resistant Escherichia coli, and in the preparation of cleaning agents or disinfectants for removing multidrug-resistant Escherichia coli contamination from object surfaces.
[0006] To achieve the above objectives, the present invention is implemented through the following technical solution: A depolymerase of Escherichia coli phage, Dep_G_1, is prepared from Escherichia coli phage vB_Eco_G1. The amino acid sequence of the phage depolymerase Dep_G_1 is shown in SEQ ID NO: 1, and the nucleotide sequence of Dep_G_1 is shown in SEQ ID NO: 2.
[0007] Furthermore, the *Escherichia coli* bacteriophage vB_Eco_G1 strain is deposited at the Guangdong Provincial Center for Microbial Culture Collection, with accession number GDMCC NO: 67745, and the deposit date is February 23, 2026.
[0008] A method for preparing the depolymerase Dep_G_1 of Escherichia coli bacteriophage, characterized by the following specific steps: 1) Using phage vB_Eco_G1 genomic DNA as a template, the Dep_G_1 gene was amplified by PCR and ligated with a vector to obtain a recombinant plasmid; 2) Transform the recombinant plasmid into the expression host bacteria, culture the expression host bacteria to induce expression, and collect the bacterial cells by centrifugation after induction; 3) Resuspend the bacterial cells in pre-cooled lysis buffer, sonicate the resuspended solution, and collect the supernatant; 4) The depolymerase Dep_G_1 was obtained by separation and purification using nickel affinity chromatography medium.
[0009] Further, in step 1), the vector is pET28a(+), and the obtained recombinant plasmid is pET28a-Dep_G_1.
[0010] Furthermore, in step 2), the expression host bacterium is Escherichia coli Rosetta (DE3).
[0011] Further, in step 3), 1 mM benzyl sulfonyl fluoride is added to the resuspended solution, and the solution is placed in an ice-water bath and broken up using an ultrasonic homogenizer with a power of 125 W. The ultrasonic treatment lasts for 5 seconds, followed by a 7-second interval, until the bacterial solution becomes clear. The bacterial solution is then centrifuged at 4 °C and 10,000 × g for 60 minutes, and the supernatant is collected.
[0012] Escherichia coli phage depolymerase Dep_G_1 is used in the preparation of formulations that inhibit or lyse multidrug-resistant Escherichia coli.
[0013] Escherichia coli phage depolymerase Dep_G_1 is used in the preparation of cleaning agents or disinfectants to remove multidrug-resistant Escherichia coli contamination from object surfaces.
[0014] The beneficial effects of this invention are: This invention is the first to identify and express the depolymerase Dep_G_1 from bacteriophage vB_Eco_G1. The depolymerase Dep_G_1 can form clear inhibition plaques against multidrug-resistant Escherichia coli and has direct in vitro lytic activity. This depolymerase can be used to develop antimicrobial protein preparations against multidrug-resistant Escherichia coli and can be used in the preparation of cleaning agents or disinfectants to remove multidrug-resistant Escherichia coli contamination from object surfaces. Attached Figure Description
[0015] Figure 1 This is an SDS-PAGE electrophoresis image of the purified Dep_G_1 depolymerase. Figure 2Photographs of plate lysis plaques of multidrug-resistant Escherichia coli UPEC Yn27 for depolymerase Dep_G_1; Figure 3 Photographs of lysis plaques of multidrug-resistant urinary tract pathogenic Escherichia coli UPEC Yn27 at different concentrations of depolymerase; Figure 4 Photographs of lysis plaques of highly virulent urinary tract pathogenic Escherichia coli UPEC Yn9 at different concentrations of depolymerase. Detailed Implementation
[0016] The present invention will be further described in detail below with reference to specific embodiments, but the scope of protection of the present invention is not limited to the content described.
[0017] Example 1 A depolymerase Dep_G_1 of Escherichia coli phage was prepared from Escherichia coli phage vB_Eco_G1. The vB_Eco_G1 strain is deposited at the Guangdong Provincial Microbial Culture Collection Center with accession number GDMCC NO: 67745 and deposit date: February 23, 2026.
[0018] The amino acid sequence of phage depolymerase Dep_G_1 is as shown in SEQ ID NO: 1, specifically: MSTITQFPSGNTQYRIEFDYLARTFVVVTLVNSSNPTLNRVLEVGRDYRFLNPTMIE MLVDQSGFDIVRIHRQTGTDLVVDFRNGSVLTASDLTNSELQAIHIAEEGRDQTVDLA KEYADAAGSSAGNAKDSEDEARRIAESIREAGLIGYITRRSFEKGYNVTTWSEVLLW EEDGDYYRWDGTLPKNVPAGSTPETSGGIGLGAWVSVGDAALRSQISNPEGAILYP ELQMARWRDEGDVRGWGAKGDGVTDSTENIAASLNSQKAVVASEGVFSSSGINSN YCNLDGRGSGVLSHRSSTGNYLVFNNPRTGRLSNITVESNKATDTTQGQQVSLAG GSDVTVSDVNFSNVKGTGFSLIAYPNDVPPDGLMIKGIRGSYSGYATNKAAGCVLAD SSVNSLIDNVIAKNYPQFGAVELKGTASYNIVSNVIGTDCQHVTYNGTEGSIAPSNNLI KGVVANNPKYAAVVAGKGSTNLISDVLVDYSTSDARQAHGVTVEGSDNVINNVLMT GCDGTNSLGQAQTATIARFIDTANNNYASVFPSYSATGVITFESGSTRNFVEVKHPG RRNDLLSATGTISGADTIDGTDNSNVVHAPALGQYIGSMSGRFEWRIKSMSLPSGVL TSADKYRMLADGAVSLAVGGGTSSQVRLFTSDGTYRNISLTRGNVRLPTSSTGYLQ LGSNAMTPDSTNTYALGSASRAWSGGFTQSAFTVVSDARDKTEPLNISDALLDAWS EVDFVQFQYLDRIEEKGADSARWHFGIIAQRAKEAFERHGIDAHRYGFLCFDSWDD VYEEDANGSRKLITPAGSRYGIRYEEVLILEAALMRRTIKRMQEALAVMSK The nucleotide sequence of the Dep_G_1 gene is shown in SEQ ID NO: 2, specifically: ATGTCCACGATTACACAATTCCCTTCAGGAAACACTCAGTACAGGATTGAGTTCG ACTACCTAGCCAGAACGTTTGTTGTTGTTACGCTGGTGAATAGCTCTAACCCTAC CCTGAACCGTGTACTGGAAGTTGGTCGAGATTACCGATTCCTTAACCCAACGATG ATTGAGATGTTGGTTGACCAATCAGGTTTCGACATCGTTCGTATTCACCGTCAGA CTGGAACTGACTTAGTGGTAGACTTCAGGAATGGCTCAGTGTTGACAGCTAGTG ACCTGACCAATTCAGAGCTTCAGGCTATCCATATTGCAGAAGAAGGTCGAGACCA AACGGTTGACTTAGCGAAGGAATATGCCGATGCTGCTGGTAGCTCTGCTGGCAA CGCTAAGGATAGCGAGGACGAAGCACGCCGAATCGCTGAGAGTATCAGGGAAG CTGGTCTAATTGGCTATATTACCCGTCGCTCCTTCGAGAAAGGCTACAACGTTAC AACATGGAGCGAGGTCCTGCTATGGGAAGAGGATGGTGATTATTACCGCTGGGA TGGTACGCTTCCAAAGAACGTTCCTGCTGGTTCAACTCCTGAAACTTCCGGTGG GATTGGTTTAGGTGCGTGGGGGTTAGTGTTGGTGATGCTGCTTTAAGAAGTCAGATT TCAAACCCGGAAGGGGCAATACTCTACCCGGAATTGCAGATGGCAAGATGGCGTGATGAGGGTGATGTTCGAGGCTGGGGTGCTAAAGGGGATGGTGTAACAGATAGT ACGGAGAATATAGCTGCTTCACTAAATTCTCAAAAAGCTGTCGTAGCATCAGAAG GTGTATTCTCTAGTTCTGGTATTAATAGTAATTACTGTAACTTAGACGGTAGAGGCA GTGGGGTGCTAAGTCACCGTTCCAGTACAGGTAACTACTTAGTATTTAACAATCC ACGTACAGGTCGCTTAAGTAATATTACGGTAGAAAGTAATAAGGCGACTGATACCA CTCAGGGACAGCAGGTATCTCTTGCTGGTGGCAGTGATGTTACGGTAAGTGACG TTAACTTCTCAAACGTTAAAGGTACTGGTTTCAGTTTAATCGCATACCCTAATGAT GTGCCACCTGATGGGCTTATGATTAAAGGCATTCGAGGTAGCTATTCCGGCTATG CTACTAATAAGGCGGCTGGATGCGTACTTGCTGACTCCTCAGTTAACTCCCTCAT AGATAACGTCATTGCTAAGAACTACCCTCAGTTCGGAGCTGTAGAGCTGAAAGGT ACAGCCAGTTACAACATAGTCAGTAATGTTATAGGGACAGATTGCCAGCATGTAAC CTACAACGGTACTGAAGGGTCAATAGCTCCTTCTAATAACCTTATCAAGGGGGTA GTTGCTAATAATCCTAAGTATGCAGCGGTTGTTGCAGGCAAAGGTAGTACGAACT TAATATCAGACGTGCTCGTAGATTACTCAACCTCTGATGCTAGGCAGGCTCATGG TGTTACAGTAGAAGGTTCTGATAACGTCATAAATAATGTGCTTATGACAGGGTGTGATGGTACTAACTCTTTAGGGCAAGCTCAAACTGCTACAATTGCTCGCTTTATAGAT ACAGCTAATAACAACTATGCGTCTGTATTTCCTAGCTACAGTGCTACAGGTGTTAT TACTTTCGAATCAGGTTCTACCCGTAACTTCGTAGAGGTAAAGCATCCGGGAAGG AGAAACGACCTTCTCAGTGCTACTGGTACTATTAGCGGTGCAGATACTATTGACG GCACTGATAATAGCAACGTAGTGCACGCCCCTGCATTAGGGCAGTACATAGGCA GTATGTCCGGTAGGTTCGAATGGCGGATTAAGTCCATGTCACTTCCATCAGGGGT TCTTACCTCTGCGGATAAGTACAGGATGCTTGCCGATGGGGCTGTGTCATTAGCT GTAGGCGGAGGTACTTCTTCTCAAGTACGCCTGTTCACTTCTGACGGCACTTATA GGAATATATCACTTACTAGAGGTAACGTGCGTCTTCCTACCAGTAGCACAGGTTAT TTGCAGTTAGGTTCTAATGCAATGACCCCAGATAGTACTAATACATACGCATTAGG TTCCGCAAGTCGAGCATGGTCTGGCGGTTTTACTCAATCAGCATTCACTGTTGTC TCAGATGCTAGGGATAAAACAGAGCCCCTTAATATCTCAGATGCTTTACTGGATGC TTGGTCTGAAGTTGACTTTGTGCAGTTTCAGTACTTGGACCGAATTGAGGAGAA GGGTGCAGACTCAGCTAGATGGCACTTCGGCATCATCGCTCAGCGAGCTAAGGA GGCCTTCGAACGTCATGGTATAGATGCACACCGCTATGGCTTCCTGTGCTTCGA CAGTTGGGATGATGTATACGAGGAAGATGCCAATGGCTCTCGTAAACTGATTACA CCAGCAGGTTCCCGCTACGGTATTCGTTACGAGGAAGTACTGATATTAGAGGCTG CGTTGATGCGGCGTACTATTAAGCGTATGCAGGAAGCATTAGCTGTTATGTCTAA GTGA Example 2 A depolymerase for Escherichia coli phage, Dep_G_1, is prepared by the following steps: 1) Using phage vB_Eco_G1 genomic DNA as a template, the Dep_G_1 gene was amplified by PCR, the pET28a(+) vector was linearized by PCR, and homologous arms were added to the ends of the primers. The recombinant plasmid pET28a-Dep_G_1 was obtained through homologous recombination. 2) The recombinant plasmid pET28a-Dep_G_1 was transformed into the expression host bacterium Rosetta(DE3). Single colonies were picked and inoculated into LB liquid medium containing 50 μg / mL kanamycin and 25 μg / mL chloramphenicol. The culture was shaken at 37°C until the OD600 was about 0.6-0.8. IPTG was added to a final concentration of 0.5 mM, and expression was induced at 37°C and 180 rpm for 6 hours. After induction, the bacterial cells were collected by centrifugation at 4°C and 5000×g for 10 minutes. 3) Resuspend the bacterial cells in pre-cooled lysis buffer (50 mM NaH2PO4, 300 mM NaCl, 10 mM imidazole, pH 8.0) at a ratio of approximately 1:10 (g / mL) of wet weight to lysis buffer volume. Add 1 mM benzyl sulfonyl fluoride to the resuspended solution. Place the bacterial suspension in an ice-water bath and use an ultrasonic homogenizer to homogenize the cells (125 W power, 5 seconds of sonication followed by 7 seconds of rest) until the bacterial solution becomes clear. Centrifuge the homogenate at 4°C and 10000×g for 60 minutes. Collect the supernatant and place it on ice for later use. 4) Take an appropriate amount of nickel affinity chromatography medium (Ni-NTA Beads) into a centrifuge tube, wash three times with 5 times the medium volume of lysis buffer to equilibrate the medium. Mix the supernatant obtained in step 3) with the equilibrated medium and incubate at 4°C on a rotary mixer for 2-3 hours to allow the histidine-tagged Dep_G_1 protein to bind fully. After incubation, centrifuge at 4°C and 1000×g for 1 minute, collect the supernatant as the flow-through buffer, and then wash the medium six times with 5 times the medium volume of wash buffer (Wash Buffer: 50 mM NaH2PO4, 300 mM NaCl, 20 mM imidazole, pH 8.0) to remove non-specifically bound proteins. Finally, add 1.2 mL of elution buffer (Elution Buffer: 50 mM NaH2PO4, 300 mM NaCl, 250 mM imidazole, pH 8.0) and incubate at 4°C for 10-15 minutes. Centrifuge at 4°C and 1000×g for 1 minute to dissociate the target protein from the medium, and collect the eluent containing the target protein.
[0019] The purified protein sample was analyzed by SDS-PAGE electrophoresis. The results are as follows: Figure 1 As shown, a single, clear band is visible at approximately 91 kDa. This band position is consistent with the predicted fusion molecular weight of the Dep_G_1 recombinant protein with the His-SUMO tag after self-cleavage of the ICA domain, indicating that high-purity recombinant Dep_G_1 protein was successfully obtained.
[0020] The Dep_G_1 obtained in this embodiment has the following potential application value: 1. Antibacterial agents: These can be further developed into topical medications (such as sprays and gels) or systemic medications for the treatment of skin and soft tissue infections, urinary tract infections, etc., caused by these multidrug-resistant bacteria.
[0021] 2. Disinfection products: can be added to medical device (such as catheter) cleaning solutions or environmental surface disinfectants to specifically eliminate contamination by multidrug-resistant E. coli and reduce the risk of hospital-acquired infections.
[0022] 3. Detection reagents: Utilizing their specific lytic activity, kits for the rapid detection of specific multidrug-resistant Escherichia coli in samples can be developed. Experimental Analysis 1. In vitro cleavage activity assay of depolymerase Dep_G_1 The activity of Dep_G_1 was detected using the spot assay method. 1) Mix 100 μL of clinically isolated multidrug-resistant Escherichia coli UPEC Yn27 overnight culture with 3-4 mL of melted semi-solid LB agar (0.5% agar), pour the mixture onto LB solid plates to make a double-layer plate.
[0023] 2) After the top layer of agar has completely solidified, use a sterile pipette tip to drop 10 μL of 2 mg / mL agar onto the surface of the plate. Dep_G_1 protein solution (set up two parallel spots) and 10 μL 0.2 mg / mL Dep_G_1 protein solution (set up two parallel spots).
[0024] 3) Place the plate in a 37°C incubator overnight (approximately 12-16 hours).
[0025] Experimental Results: As shown in Figure 2, clear and distinct transparent lysis plaques were formed at both sites where 2 mg / mL Dep_G_1 protein solution was added and at the site where 0.2 mg / mL Dep_G_1 protein solution was added. This result indicates that the recombinant depolymerase Dep_G_1 has clear lytic activity against this multidrug-resistant Escherichia coli strain at a concentration of 2 mg / mL.
[0026] To determine the minimum protein concentration at which the depolymerase Dep_G_1 exerts its cleavage activity, the following experiments were performed: 1) The purified Dep_G_1 protein was serially diluted with PBS buffer to prepare protein solutions with concentrations of 1 mg / mL, 0.1 mg / mL, 0.01 mg / mL, 1 μg / mL, 0.1 μg / mL, 0.01 μg / mL, 1 ng / mL, 0.1 ng / mL, and 0.01 ng / mL.
[0027] 2) Using the plaque lysis method: Mix 100 μL of overnight culture of multidrug-resistant Escherichia coli UPEC Yn27 with 3-4 mL of semi-solid LB agar and pour it onto an LB solid plate.
[0028] 3) After the plate solidifies, add 10 μL of Dep_G_1 protein solution of different concentration gradients to the surface.
[0029] 4) Place the plate in a 37℃ incubator and incubate for 12-18 hours.
[0030] Experimental results: such as Figure 3 As shown, Dep_G_1 protein formed obvious transparent lysis plaques at concentrations of 0.1 μg / mL and above; when the concentration decreased to 0.01 μg / mL, the lysis plaques disappeared or only faint traces were visible. These results indicate that the minimum effective concentration (MEC) of the depolymerase Dep_G_1 for the test strain UPEC Yn27 is approximately 0.1 μg / mL.
[0031] The bioactivity of depolymerase Dep_G_1 against another highly virulent urinary tract pathogenic Escherichia coli (UPEC) strain UPEC Yn9 was detected by the spot assay method, and its minimum effective concentration was determined.
[0032] 1) Serial dilution: The purified Dep_G_1 protein was serially diluted with PBS buffer to prepare protein solutions with concentrations of 1 mg / mL, 0.1 mg / mL, 0.01 mg / mL, 1 μg / mL, 0.1 μg / mL, 0.01 μg / mL, and 1 ng / mL.
[0033] 2) Preparation of double-layer plates: Mix 100 μL of overnight culture of highly virulent Escherichia coli UPEC Yn9 with 3-4 mL of melted semi-solid LB agar (0.5% agar) and pour the mixture onto an LB solid plate. Spotting: After the plate has solidified, add 10 μL of Dep_G_1 protein solution at various concentration gradients to the surface of the agar.
[0034] 3) Culture and observation: Place the plates in a 37℃ incubator and incubate for 12-18 hours. Observe the formation of transparent lysis spots (or halos) under each dilution gradient.
[0035] Experimental results: such as Figure 4 As shown, the recombinant depolymerase Dep_G_1 exhibits extremely high lytic activity against the highly virulent strain UPEC Yn9: clear and transparent lysis plaques are formed at the droplet concentration of 0.1 μg / mL and above, while no obvious lysis plaques or halos are observed by the naked eye when the concentration is reduced to 0.01 μg / mL.
[0036] This indicates that the depolymerase Dep_G_1 can not only act on common multidrug-resistant bacteria, but also has significant biological activity against highly virulent urinary tract pathogenic Escherichia coli UPEC Yn9.
[0037] Finally, it should be noted that the above preferred embodiments are only used to illustrate the technical solutions of the present invention and are not intended to limit it. Although the present invention has been described in detail through the above preferred embodiments, those skilled in the art should understand that various changes can be made to it in form and detail without departing from the scope defined by the claims of the present invention.
Claims
1. A depolymerase Dep_G_1 for Escherichia coli bacteriophage, characterized in that: The phage depolymerase Dep_G_1 was prepared from Escherichia coli phage vB_Eco_G1. The amino acid sequence of the phage depolymerase Dep_G_1 is shown in SEQ ID NO: 1, and the nucleotide sequence of Dep_G_1 is shown in SEQ ID NO:
2.
2. The depolymerase Dep_G_1 of Escherichia coli bacteriophage according to claim 1, characterized in that: The *Escherichia coli* bacteriophage vB_Eco_G1 strain is deposited at the Guangdong Provincial Center for Microbial Culture Collection, with accession number GDMCCNO: 67745, and the deposit date is February 23, 2026.
3. The method for preparing the depolymerase Dep_G_1 of Escherichia coli bacteriophage according to claim 1, characterized in that: The specific steps include: 1) Using phage vB_Eco_G1 genomic DNA as a template, the Dep_G_1 gene was amplified by PCR and ligated with a vector to obtain a recombinant plasmid; 2) Transform the recombinant plasmid into the expression host bacteria, culture the expression host bacteria to induce expression, and collect the bacterial cells by centrifugation after induction; 3) Resuspend the bacterial cells in pre-cooled lysis buffer, sonicate the resuspended solution, and collect the supernatant; 4) The depolymerase Dep_G_1 was obtained by separation and purification using nickel affinity chromatography medium.
4. The method for preparing the depolymerase Dep_G_1 of Escherichia coli bacteriophage according to claim 3, characterized in that: In step 1), the vector is pET28a(+), and the obtained recombinant plasmid is pET28a-Dep_G_1.
5. The method for preparing the depolymerase Dep_G_1 of Escherichia coli bacteriophage according to claim 3, characterized in that: In step 2), the expression host bacterium is Escherichia coli Rosetta (DE3).
6. The method for preparing the depolymerase Dep_G_1 of Escherichia coli bacteriophage according to claim 3, characterized in that: In step 3), add 1mM benzyl sulfonyl fluoride to the resuspended solution, place it in an ice-water bath, and break it up with an ultrasonic homogenizer with a power of 125W. The ultrasonic operation is 5 seconds, followed by a 7-second interval, until the bacterial solution becomes clear. The bacterial solution is centrifuged at 4℃ and 10000×g for 60 minutes, and the supernatant is collected.
7. The application of the Escherichia coli phage depolymerase Dep_G_1 as described in claim 1 in the preparation of formulations that inhibit or lyse multidrug-resistant Escherichia coli.
8. The application of the Escherichia coli phage depolymerase Dep_G_1 as described in claim 1 in the preparation of a cleaning agent or disinfectant for removing multidrug-resistant Escherichia coli contamination from object surfaces.