CN116410935A - Cross-family-infection multivalent vibrio parahaemolyticus phage vB_VpaP_G1 and application thereof - Google Patents
Cross-family-infection multivalent vibrio parahaemolyticus phage vB_VpaP_G1 and application thereof Download PDFInfo
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- C—CHEMISTRY; METALLURGY
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- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
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- A—HUMAN NECESSITIES
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- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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Abstract
The invention belongs to the technical field of biology, and discloses a cross-family infectious multivalent vibrio parahaemolyticus phage vB_VpaP_G1 and application thereof, wherein G1 is a cross-family bacterial multivalent phage, and can crack bacteria such as Cronobacter, salmonella, escherichia coli, yersinia small intestine and Aeromonas caviae from the Enterobacteriaceae besides the Vibrio parahaemolyticus of the Vibrio, can be used as an antibacterial agent for preventing and treating various bacteria, effectively solves the problem of drug resistance faced by the current antibiotic treatment, and has good utilization value and application prospect.
Description
Technical Field
The invention belongs to the technical field of biology, and particularly relates to a cross-family infectious multivalent vibrio parahaemolyticus phage vB_VpaP_G1 and application thereof.
Background
Vibrio parahaemolyticus (Vibrio parahaemolyticus) is a halophilic gram-negative bacterium belonging to the genus Vibrio of the family Vibrionaceae, and is widely distributed in fish, shrimp and shellfish in estuaries and oceans worldwide. People often cause diarrhea, fever, gastroenteritis, and the like by eating fresh, insufficiently boiled or cross-contaminated aquatic products contaminated with vibrio parahaemolyticus. According to the prior report, the food poisoning event caused by the vibrio parahaemolyticus occupies the first place of the food poisoning event, seriously harms the physical health of people and causes huge economic loss. Antibiotic treatment is the most dominant means for preventing and treating bacterial infection, however, in recent years, the irregular abuse of antibiotics for a long time causes great burden on clinical treatment and social economy, and because of the broad-spectrum disinfection property of antibiotics, irreversible damage is caused to the ecological system of the original microorganisms, and finally the ecological system of the original microorganisms can threaten the health of human bodies, thus becoming a global public health safety problem, and therefore, the search for alternative therapies of antibiotics is urgent for coping with the bacterial drug resistance problem.
Phage exist widely in nature, can specifically cause the lysis of host cells to cause bacterial death, and provides a new means for controlling food-borne pathogenic bacteria. The phage does not destroy the balance of a micro-ecological system due to the host specificity, is safe to human and animals, is not easy to generate tolerance, has the advantage of being superior to antibiotics in the aspect of controlling pathogenic bacteria, and gradually becomes an alternative to the antibiotics and is applied to the market. The phage has high specificity, but in recent years, the academic world discovers that some phages have a certain broad-spectrum cracking capability against host bacteria among different species, the phages are changed into multivalent phages, and the technology of synchronously inactivating various pathogenic bacteria by using the multivalent phages has the advantages of broad-spectrum high performance, safety, high efficiency and environmental friendliness, so the discovery lays a solid theoretical foundation for the wide application of the phages.
There are some limitations in phage application and phage therapy.
Firstly, bacteriophages have been promising for the treatment of bacterial infections by replacing antibiotics because of their specificity for host bacteria, so that they do not harm other bacteria while killing the host bacteria, however, the bacteria in nature are of a wide variety, and the narrow spectrum of bacteriophages is difficult to control multiple bacterial mixed infections, as this makes their use difficult to break through.
Secondly, some phages have lysogenic capacity, and during the life cycle of lysogenic phages, i.e. temperate phages, their DNA co-propagates with the bacteria mainly in such a way as to integrate into the chromosomes of the bacteria, and only in the event of adversity stress will enter the lysis cycle. This leads to two problems, namely, the inability to kill pathogenic bacteria rapidly; secondly, gene level transfer may be caused, and bacterial pathogenic genes may be integrated into the phage genome, resulting in transmission of pathogenic genes between strains.
Finally, the stability of phage preparations can be an important factor in their practical use, phage preparations must maintain phage titers within a useful range during shipping and sales, and phage must ensure stable survival and function in the environment of the application in which they are put.
Therefore, the key to solving these limitations is to find phage with a wide cleavage spectrum and capable of cleaving vibrio parahaemolyticus of various serotypes, and to find phage without lysogenic genes and virulence factors and capable of producing better disinfecting and preventing effects so as to be safely applied to practical production.
Disclosure of Invention
The invention aims to overcome the defect of narrow phage lysis spectrum in the prior art, provides a novel vibrio parahaemolyticus phage vB_VpaP_G1 (hereinafter referred to as G1), is a multivalent phage capable of crossing a infected host, has a wider host spectrum, has better killing and preventing effects on bacteria of vibrio, aeromonas, enterobacteriaceae and yersinia, does not contain soluble genes and virulence genes, and can be applied to the research and development of antibacterial agents.
A second object of the present invention is to provide the use of phage G1 as described above.
The aim of the invention is realized by the following technical scheme:
the invention firstly provides a Vibrio parahaemolyticus phage vB_VpaP_G1, which is classified and named as Vibrio phase, and the phage is preserved in the microorganism strain collection in Guangdong province at 2023, 1 month and 5 days, and the preservation number is GDMCC NO:63110-B1, the preservation address is: guangzhou city first middle road No. 100 college No. 59 building 5.
The phage is separated from a water sample of a sewer of the Guangzhou yellow sand aquatic market by adopting a sedimentation-filtration method, the host is O11-56, the tolerance range of the phage pH is pH 5-11, and the phage can tolerate the high temperature of 60 ℃, and the phage is named as vB_VpaP_G1 (hereinafter abbreviated as G1).
Specifically, the composition can be a pharmaceutical composition or a bactericidal composition.
The invention also provides application of the vibrio haemolyticus phage vB_VpaP_G1, wherein the specific application comprises the following steps:
(1) Inhibiting the proliferation of vibrio parahaemolyticus, aeromonas, salmonella, streptococcus pneumoniae, escherichia coli, cronobacter, yersinia enteritis;
(2) Killing vibrio parahaemolyticus, aeromonas, salmonella, streptococcus pneumoniae, escherichia coli, cronobacter, yersinia enteritis;
(3) Preventing and treating pollution caused by vibrio parahaemolyticus, aeromonas, salmonella, streptococcus pneumoniae, escherichia coli, cronobacter and yersinia enteritis;
(4) Preparing medicine for treating diseases caused by infection of vibrio parahaemolyticus, aeromonas, salmonella, streptococcus pneumoniae, escherichia coli, cronobacter and yersinia enteritis.
Preferably, the disease is selected from the group consisting of acute diarrhea, sepsis, salmonellosis, bronchitis, pneumonia, urinary system wound infection, meningitis, peritonitis, bacteremia, necrotizing enterocolitis. The invention provides an environment-friendly new medicine for preventing and controlling diseases caused by the bacterial infection.
Preferably, in the above application, the bactericidal composition can be a water disinfectant, so that the bactericidal composition is applied to the processes of aquatic product cultivation, transportation and preservation. More preferably, the concentration thereof is not less than 10 5 pfu/mL. At this concentration, the disinfection effect of the water disinfectant is optimal. It is of course foreseeable that the water body disinfectant also comprises other matched bactericidal activity agents or adjuvants.
Preferably, in the above application, the bactericidal composition and/or the pharmaceutical composition can also be a feed additive, and the phage or the phage-containing food can be used as a feed additiveThe phage composition can be added into feed for aquatic animals such as Penaeus vannamei Boone to effectively increase survival rate of young shrimp, and the phage content in feed additive is not less than 10 5 pfu/mL。
The invention also provides a culture method of the vibrio parahaemolyticus phage vB_VpaP_G1, which comprises inoculating the vibrio parahaemolyticus phage vB_VpaP_G1 into a liquid culture medium, culturing to a logarithmic phase, and then inoculating phage for phage culture.
Compared with the prior art, the invention has the following advantages:
the invention provides a vibrio parahaemolyticus phage named as vB_VpaP_G1, wherein the vibrio parahaemolyticus phage G1 has a short incubation period (10 min) for vibrio parahaemolyticus, can be amplified through a specific host, can resist high temperature of 60 ℃, resist pH 5.0-pH 11.0, and is inactivated after being irradiated by an ultraviolet lamp for 30min, has high stability, has low requirements on transportation and preservation, and can be suitable for being used in environments with different conditions. Most notably, G1 is a multivalent phage capable of cross-family bacterial lysis, can crack bacteria such as Cronobacter, salmonella, escherichia coli, yersinia small intestine and Aeromonas caviae from Enterobacteriaceae besides Vibrio parahaemolyticus from Vibrionaceae, can be used as an antibacterial agent for preventing and treating various bacteria, effectively solves the problem of drug resistance faced by the current antibiotic treatment, and has good utilization value and application prospect.
Drawings
FIG. 1 is a phage G1 electron microscope image;
FIG. 2 is a phage G1 VIDIRIIC sequence alignment;
FIG. 3 is a graph of phage G1 protein sharing network analysis;
FIG. 4 is a bacteriophage G1 phylogenetic tree;
FIG. 5 is a phage G1 MOI;
FIG. 6 shows phage G1 temperature stability;
FIG. 7 is the pH stability of phage G1;
FIG. 8 is phage G1 UV tolerance;
FIG. 9 shows a one-step growth curve of phage G1.
Detailed Description
The invention will be further described in detail below with reference to the drawings of embodiments of the invention, and the description is not intended to limit the invention described in the claims. It will be apparent that the embodiments described are only critical embodiments and not all embodiments, as will be readily appreciated by those skilled in the art.
EXAMPLE 1 isolation culture of phages
1. Activation and cultivation of host bacteria
The food-borne vibrio parahaemolyticus, cronobacter, salmonella, yersinia enteritis, escherichia coli, listeria, staphylococcus aureus, aeromonas, bacillus and the like used in the study are provided by the Guangdong microbiological study, a dry powder tube is taken out from a refrigerator at 4 ℃, a tube orifice is smashed, a sterile gun head is taken out and added into 3% sodium chloride alkaline peptone water, the mixture is placed in a shaking table at 37 ℃ for culturing for 24 hours, and after the identification by a chromogenic plate streak, single colony is selected and inoculated into 5mL of liquid culture medium at 37 ℃ for culturing for 24 hours, so that single suspension is obtained.
2. Isolation and purification of phages
Collecting water sample from yellow sand aquatic product trade market sewer in Guangzhou city in 6 months in 2020, centrifuging the sewage sample at room temperature for 10min, filtering the supernatant with a 0.45 μm filter, adding solid anhydrous magnesium sulfate to a final concentration of 50mM, mixing, standing at room temperature for 10-20 min, using a suction filtration device, passing the mixed solution through a 0.45 μm cellulose filter membrane, taking the filter membrane, placing the filter membrane into phage eluent, performing ultrasonic elution, filtering the eluent with the 0.45 filter, and storing the filtrate at 4 ℃ for later use. Mixing the above filtrate and logarithmic phase host suspension, adding 4mM CaCl 2 In the two-component TSB of (C), the culture was conducted through a 0.45 μm filter after 24 hours of culture, to obtain a phage-filtered culture broth. Identifying whether phage in phage filtration culture solution contains phage by double-layer plate method, and selecting the phageAnd (3) purifying the filtered culture solution of the target host phage for multiple times by using a double-layer plate method, and finally forming plaques with consistent size and morphology on a culture medium, namely finishing the purification. This phage is designated as vB_VpaP_G1 (hereinafter abbreviated as G1).
EXAMPLE 2 identification of phage
1. Morphological identification of phages
15 μl of 1×10 is taken 10 Dropping the pfu/mL phage sample onto a microporous copper net, naturally settling for 15min, absorbing excessive liquid by using filter paper, dropping 10 mu l phosphotungstic acid (2%) for 5min, absorbing excessive liquid by using filter paper, naturally drying, searching phage particles by using a transmission electron microscope, observing the morphology of the phage particles, and recording by photographing, wherein the phage G1 has an icosahedral head and a short tail without shrinking, and has a head diameter of 34+/-2 nm and a tail length of 12+/-2 nm, and the specific picture is shown in figure 1. Phage G1 met the typical characteristics of Caudoviricetes Podoviridae according to its morphological characteristics combined with the formal classification rules of ICTV.
2. Molecular biological identification of phages
(1) Genome extraction of phage G1
Phage were concentrated using PEG-NaCl method and allowed to stand overnight at 4 ℃. The next day, 12000 Xg, 20 min. The pellet was resuspended with SM buffer. Concentrating the obtained phage, extracting phage DNA with phenol, chloroform and isoamyl alcohol, and preserving at-20deg.C for use.
(2) Phage G1 whole genome sequencing and whole genome feature analysis thereof
The concentration of the extracted DNA was determined using a fluorescent quantiter Qubit 3.0Fluorometer, 100ng of the DNA samples described above were taken, phage DNA libraries were constructed using a QIAseq FX DNA Library Kit kit, and sequenced on an Illumina NextSeq 550 (Illumina, USA) sequencing platform. Sequence assembly and splicing was performed on sequencing libraries using SPAdes software. And (5) aligning the final splicing result on NCBI. Phage G1 is a short tail virus with RNA polymerase. Thus, initially classifying G1 as Autographividae, phage G1 showed the highest homology (73.01%) with phage phiR8-01 (NC_ 047951.1), but had very low genome coverage (19%). BLASTN and ANI results indicate that the coverage of the G1 genome with phiR8-01 genome is too low and that the similarity results are less reliable, so that phage G1 was re-analyzed for genomic similarity with other phages using the VIRIDIC. The virdic results showed that G1 had a maximum similarity of 47.1% with other known sequences (fig. 2). The international classification of viruses (ICTV) describes a genus as a group of viruses with high similarity, sharing at least 60-70% nucleotides over the entire genome length, with G1 being much less similar to other sequences than this threshold. To further clarify the taxonomic status of G1, analysis of the phage protein sharing network revealed that vConTACT analysis revealed that vB_VpaP_G1 formed a subset of VC clusters with the Melnykvirinae phage (FIG. 3) and was further supported by phylogenetic trees terminating large subunits of enzymes (FIG. 4). Phage G1 was therefore suggested to establish a Youngvirus genus under the Melongkvirinae subfamily, with G1 being defined as a new species in this new genus.
The characteristics of phage G1 are briefly described in Table 1, phage G1 being annotated to a total of 50 ORFs, of which 74.0% ORFs (37/50) can be annotated to proteins of known function, which ORFs can be divided into structural, nucleic acid metabolism, packaging, cleavage, DNA injection, anti-defenses and other domains.
The structural functional domains include: outer capsid protein, DNA maturation enzyme a, tail forming protein, tail fiber protein, structural protein, tail tube protein B, tail tube protein a, main capsid protein, scaffold protein, head-tail junction protein, etc.
Nucleic acid metabolic domains include: DNA helicase, DNA primer enzyme, ribosomal like regulator protein.
N-acyltransferase superfamily proteins, RNA polymerase, ATP binding proteins, DNA endonucleases.
DNA exonucleases, DNA polymerases, DNA ligases, and the like.
The packaging function domain includes: a large terminal enzyme subunit and a small terminal enzyme subunit, it is believed that the large terminal enzyme subunit is involved in DNA cleavage, while the small terminal enzyme subunit is involved in recognition and binding of concatemeric DNA.
The cleavage domain comprises: phage lysin, perforin and spin proteins. Lysin is a phage-encoded lytic enzyme that aids in the release of progeny phage from bacterial cells by cleaving peptidoglycans of the bacterial cell wall. The function of perforin is to form a tubular channel of polyperforin on the cell membrane, resulting in lytic destruction.
The DNA injection domain includes: cleavage of the transglycosidase active protein, internal core protein a, internal core protein.
The back defense includes: silencing protein inhibitor, S-adenosylmethionine lyase and S-adenosylmethionine lyase
TABLE 1 functional classification of phage G1 Whole genome open reading frame
Example 3 phage G1 biological Property detection
1. Phage G1 potency assay
Determination of phage titer by double-layer plate method, firstly, continuously diluting purified phage culture-expanding solution by 10 times, selecting proper dilution, respectively sucking 100 μl phage dilution and 100 μl Vibrio parahaemolyticus O11-56 bacterial liquid cultured to logarithmic phase, simultaneously adding TSB (containing 0.4% technical agar, 2mM CaCl) cooled to 45 deg.C 2 ) Well mixed and poured onto TSA plates, 3 replicates of each dilution were made. After the soft agar is solidified, placing the soft agar into a constant temperature incubator at 37 ℃ for culturing for 5-8 hours, observing and counting the plates with the plaque number of 30-300, and calculating to obtain the titer of the phage G1 of 2.57 multiplied by 10 9 pfu/mL。
2. Phage G1 optimal multiplicity of infection (MOI) assay
Phage G1 and Vibrio parahaemolyticus O11-56 were propagated according to conventional methods, phage and host cell titers were determined and configured in different ratios (100, 10,1,0.1,0.01,0.001 and 0.000)1) Phage-logarithmic phase vibrio parahaemolyticus bacterial liquid, wherein the concentration of host bacteria is 10 8 cfu/mL, added to TSB culture broth (containing 2mM CaCl) 2 ) Culturing in shaking table at 37deg.C and 200rpm/min, filtering the culture solution with 0.45 μm filter after 10 hr, selecting phage dilution with proper gradient, measuring phage titer with double-layer plate method, and performing three independent experiments. The results in FIG. 5 show that phage vB_ VpP _G1 has an optimal MOI=1 and phage titer of 8×10 7 pfu/mL。
3. Host bacterium of phage G1
Adding 100 μl of log phase bacterial liquid into 5ml of 0.4% TSA soft agar, mixing, pouring onto 1.5% TSA solid plate, adding 2 μl of phage G1 culture liquid dropwise onto soft agar, and making five gradients of phage G1 dilution (10 10 ,10 9 ,10 8 ,10 7 ,10 6 ,10 5 pfu/mL) and labeled, placed in an incubator at 37 ℃ for culturing, and after 5 hours, observed and recorded whether plaque appeared or not, thereby confirming phage G1 host profile. As shown in Table 2, the host profile of the strain from 15 species of 11 genus of 7 family was identified, and the result showed that G1 was able to lyse 17 strains of Vibrio parahaemolyticus (17/124), the lysis rate was 13.7%. G1 also can crack 3 strains of aeromonas (3/20) of aeromonas, and the cracking rate is 15%; salmonella strain 19 (19/35) of Enterobacteriaceae, cleavage efficiency of 54.3%; 9 strains of streptococcus pneumoniae of enterobacteriaceae, the cracking rate is 30%; 12 strains of Escherichia coli belonging to the Enterobacteriaceae family, and a lysis rate of 42.8%; 56 Cronobacter (56/69) strains of Enterobacteriaceae with a lysis rate of 81.2%;7 yersinia enteritis strains (7/186), lysis rate was 3.8%.
TABLE 2 host ranges of phages vB_VpaP_G1
4. Determination of phage G1 for temperature, pH, UV stability
1mL phage suspension (1X 10) was added to each of the 1.5mL EP tube-in-tube 8 pfu/mL), incubated in different water bath temperatures (25, 37, 50, 60 and 70 ℃) for 1h, cooled to room temperature immediately after the end, phage suspension titers were detected by the double-layer plate method, and three independent experiments were performed. Specific results referring to FIG. 6, phage G1 remained essentially unchanged in titer after treatment at 25℃to 50℃for 1 hour, reduced in titer by about 3 lg values after treatment at 60℃for 1 hour, and completely inactivated after 45min in a water bath at 70 ℃. Therefore, phage G1 has better heat stability.
For phage pH determination, filter sterilization was performed with disposable syringes and 0.45 μm filter heads by TSB broth configured to different pH values (3, 4,5,6,7,8,9, 10, 11, 12). 0.1mL phage lysate (1X 10) 8 pfu/mL) was added to 0.9mL of TSB of different pH, incubated at 37 ℃ for 1h, taken out, phage titers were detected by double-layer plate method, and three independent experiments were performed. Specific results referring to fig. 7, phage G1 was able to exist stably in the pH range of 5 to 11, and phage titer was reduced by 3 lg values when ph=4, peracid, to ph=3, and phage were completely inactivated. When ph=12, the phage were all inactivated when overbased.
In phage ultraviolet UV 245 tolerance assay, phage suspensions (1X 10 8 pfu/mL) was added to a sterile petri dish and the samples were placed 15cm from the uv lamp in a biosafety cabinet, 100 μl of sample solution was aspirated every 5min from 0min, the phage titer was determined by double-plate method, and three independent experiments were performed. Specific results referring to fig. 8, phage G1 was relatively sensitive to uv, with a significant decrease in phage titer every 5 min. When the ultraviolet irradiation is carried out for 5min, the titer is greatly reduced by 2 lg values, the total titer is reduced by 6 lg values at 20min, and the phage is completely killed after 30 min.
5. Phage G1 one-step growth curve
100. Mu.L of the overnight culture of Vibrio parahaemolyticus was inoculated to 5mL of TSB, and cultured in a shaking table at a constant temperature of 37℃and 200rpm/min to OD 600 =0.2, and bacterial cells were taken upThe suspension was diluted to 1X 10 8 pfu/mL, 1mL of bacterial culture was aspirated with a pipette, the supernatant was aspirated by centrifugation at 8000g for 5min, care was taken to avoid aspiration of bacterial pellet, resuspended in 0.9mL SM buffer, and combined with 100. Mu.L of 1X 10 8 pfu/mL phage suspension (MOI=0.1), add CaCl 2 To a final concentration of 2mM, thoroughly mixed, the mixture was allowed to stand at 37℃for 15min, after centrifugation at 12000g for 2min, the supernatant free phage was removed, and the bacterial host pellet was resuspended in 10mL TSB (2 mM CaCl) 2 ) In the above, the mixture was then placed on a constant temperature shaker and cultured with shaking at 37℃and 200rpm/min, 100. Mu.L of the sample solution was aspirated every 5min from 0min, and phage titer was determined by the double-layer plate method. Specific results referring to FIG. 9, the G1 latency was 10min, the lysis period was 25min, and the amount of lysis was 29pfu/cell. Although phage G1 latency is relatively short, it may be able to have some inhibitory effect on the initial growth of Vibrio parahaemolyticus.
The embodiments of the present invention have been described in detail above, but the present invention is not limited to the described embodiments. It will be apparent to those skilled in the art that various changes, modifications, substitutions and alterations can be made to these embodiments without departing from the principles and spirit of the invention, and yet fall within the scope of the invention.
Claims (4)
1. Use of vibrio parahaemolyticus phage vb_vpap_g1, characterized in that the use comprises:
(1) Inhibiting the proliferation of vibrio parahaemolyticus, aeromonas, salmonella, streptococcus pneumoniae, escherichia coli, cronobacter, yersinia enteritis;
(2) Killing vibrio parahaemolyticus, aeromonas, salmonella, streptococcus pneumoniae, escherichia coli, cronobacter, yersinia enteritis;
(3) Preventing and treating pollution caused by vibrio parahaemolyticus, aeromonas, salmonella, streptococcus pneumoniae, escherichia coli, cronobacter and yersinia enteritis;
(4) Preparing a medicament for treating diseases caused by infection of vibrio parahaemolyticus, aeromonas, salmonella, streptococcus pneumoniae, escherichia coli, cronobacter and yersinia enteritis;
the phage vB_VpaP_G1 was deposited at the microorganism strain collection in Guangdong province at 2023, 1/5, under the accession number GDMCC NO:63110-B1, the preservation address is: guangzhou city first middle road No. 100 college No. 59 building 5.
2. The use according to claim 1, wherein the disease is selected from the group consisting of acute diarrhea, sepsis, salmonellosis, bronchitis, pneumonia, urinary system wound infection, meningitis, peritonitis, bacteremia, necrotizing enterocolitis.
3. The use according to claim 1, wherein the composition comprises a pharmaceutical composition and a bactericidal composition.
4. The use according to claim 3, wherein the pharmaceutical composition is a feed additive and the bactericidal composition is a water disinfectant.
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