Analysis of genomic information and biological characteristics of a bacteriophage against methicillin-resistant Staphylococcus aureus in patients with median sternal incision infection / 中华烧伤杂志

Objective: To isolate and purify a bacteriophage against methicillin-resistant Staphylococcus aureus (MRSA), and to analyze its genomic information and biological characteristics. Methods: The experimental research methods were adopted. MRSA (hereinafter referred to as host bacteria) solution was collected from the wound of a 63-year-old female patient with the median sternum incision infection admitted to the Second Affiliated Hospital of Army Medical University (the Third Military Medical University). The bacteriophage, named bacteriophage SAP23 was isolated and purified from the sewage of the Hospital by sewage co-culture method and double-layer agar plate method, and the plaque morphology was observed. The morphology of bacteriophage SAP23 was observed by transmission electron microscope after phosphotungstic acid negative staining. The whole genome of bacteriophage SAP23 was sequenced with NovaSeq PE15 platform after its DNA was prepared by sodium dodecyl sulfonate/protease cleavage scheme, and genomic analysis including sequence assembly, annotation, and phylogenetic tree were completed. The bacteriophage SAP23 solution was co-incubated with the host bacterial solution for 4 h at the multiplicity of infection (MOI) of 10.000 0, 1.000 0, 0.100 0, 0.010 0, 0.001 0, and 0.000 1, respectively, and then the bacteriophage titer was measured by the drip plate method to select the optimal MOI, with here and the following sample numbers of 3. The bacteriophage SAP23 solution was co-incubated with the host bacterial solution at the optimal MOI for 5, 10, and 15 min, respectively, and the bacteriophage titer was measured by the same method as mentioned above to select the optimal adsorption time. After the bacteriophage SAP23 solution was co-incubated with the host bacterial solution at the optimal MOI for the optimal adsorption time, the bacteriophage titers were measured by the same method as mentioned above at 0 (immediately), 5, 10, 15, 20, 30, 40, 50, 60, 80, 100, and 120 min after culture, respectively, and a one-step growth curve was drawn. The bacteriophage SAP23 solution was incubated at 4, 37, 50, 60, 70, and 80 ℃ and pH 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12 for 1 h, respectively, to determine its stability. A total of 41 MRSA strains stored in the Department of Microbiology of Army Medical University (the Third Military Medical University) were used to determine the host spectrum of bacteriophage SAP23. Results: The bacteriophage SAP23 could form a transparent plaque on the host bacteria double-layer agar plate. The bacteriophage SAP23 has a polyhedral head with (88±4) nm in diameter and a tail with (279±21) nm in length and (22.6±2.6) nm in width. The bacteriophage SAP23 has a linear, double-stranded DNA with a full length of 151 618 bp and 11 681 bp long terminal repeats sequence in the sequence ends. There were 220 open reading frames predicted and the bacteriophage could encode 4 transfer RNAs, while no resistance genes or virulence factors were found. The annotation function of bacteriophage SAP23 genes could be divided into 5 groups. The GenBank accession number was MZ427930. According to the genomic collinearity analysis, there were 5 local collinear blocks in the whole genome between the bacteriophage SAP23 and the chosen 6 Staphylococcus bacteriophages, while within or outside the local collinear region, there were still some differences. The bacteriophage SAP23 belonged to the Herelleviridae family, Twortvirinae subfamily, and Kayvirus genus. The optimal MOI of bacteriophage SAP23 was 0.010 0, and the optimal adsorption time was 10 min. The bacteriophage SAP23 had a latent period of 20 min, and a growth phase of 80 min. The bacteriophage SAP23 was able to remain stable at the temperature between 4 and 37 ℃ and at the pH values between 4 and 9. The bacteriophage SAP23 could lyse 3 of the 41 tested MRSA strains. Conclusions: The bacteriophage SAP23 is a member of the Herelleviridae family, Twortvirinae subfamily, and Kayvirus genus. The bacteriophage SAP23 has a good tolerance for temperature and acid-base and a short latent period, and can lyse MRSA effectively. The bacteriophage SAP23 is a new type of potent narrow-spectrum bacteriophage without virulence factors and resistance genes.

Prevention and control of antimicrobial resistance using CRISPR-Cas system: a review / 生物工程学报

Bacterial multi-drug resistance (MDR) is a global challenge in the fields of medicine and health, agriculture and fishery, ecology and environment. The cross-region spread of antibiotic resistance genes (ARGs) among different species is one of the main cause of bacterial MDR. However, there is no effective strategies for addressing the intensifying bacterial MDR. The CRISPR-Cas system, consisting of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated proteins, can targetedly degrade exogenous nucleic acids, thus exhibiting high application potential in preventing and controlling bacterial MDR caused by ARGs. This review briefly introduced the working mechanism of CRISPR-Cas systems, followed by discussing recent advances in reducing ARGs by CRISPR-Cas systems delivered through mediators (e.g. plasmids, bacteriophages and nanoparticle). Moreover, the trends of this research field were envisioned, providing a new perspective on preventing and controlling MDR.

Advances of phage receptor binding proteins / 生物工程学报

Bacteriophages bind to the bacteria receptor through the receptor binding proteins (RBPs), a process that requires the involvement of complex atomic structures and conformational changes. In response to bacteriophage infection, bacteria have developed a variety of resistance mechanisms, while bacteriophages have also evolved multiple antagonistic mechanisms to escape host resistance. The exploration of the "adsorption-anti adsorption-escape process" between bacteriophages and bacteria helps us better understand the co-evolution process of bacteriophages and bacteria, which is important for the development of phage therapeutic technologies and phage-based biotechnologies. This review summarizes the bacteriophage adsorption related proteins, how bacteriophages escape host resistance based on the RBP alternations, and the recent progress of RBP-related biotechnologies.

Application of CRISPR in evolution analysis, detecting and typing, virulence and antibiotic resistance regulation in food-borne pathogens / 生物工程学报

Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated protein gene system can limit the horizontal gene transfer, thereby effectively preventing the invasion of foreign gene elements such as bacteriophages. CRISPR arrays of different bacteria are diverse. Based on the differences in the CRISPR system, this review summarizes the application of CRISPR in food-borne pathogen evolution analysis, detection and typing, virulence and antibiotic resistance in recent years. We also address bacterial detection typing method developed based on the characteristics of CRISPR arrays and the association of CRISPR with virulence and drug resistance of food-borne pathogens. The shortcomings of CRISPR in evolution, detection and typing, virulence and resistance applications are analyzed. In addition, we suggest standardizing CRISPR typing methods, improving and expanding the CRISPR database of pathogenic bacteria, and further exploring the co-evolution relationship between phages and bacteria, to provide references for further exploration of CRISPR functions.

Development of a luminescence real-time method for monitoring live bacteria during phage lysis / 生物工程学报

The toxin-producing bacterium Vibrio cholerae can cause severe diarrhea and has caused seven global pandemics. Traditional viable cell counts and phage plaques are commonly used to evaluate the efficacy of virulent phage clearance of V. cholerae, but these operations are time-consuming and labor-intensive, and difficult to provide real-time changes. It is desirable to develop a simple and real-time method to monitor V. cholerae during phage lysis. In this study, a luminescence-generating plasmid pBBR-pmdh-luxCDABE was transformed into three O1 serogroup drug-resistant strains of V. cholerae. The results showed that the luminescence value as a monitoring index correlates well with the traditional viable cell count method. Monitoring the number of live cells of V. cholerae by measuring the luminescence allowed real-time analysis of the number of bacteria remaining during phage lysis. This method enables repeated, interference-free, continuous multiple-time-point detection of the same sample without the time delay of re-culture or plaque formation, facilitating real-time monitoring and analysis of the interaction between the phage and the host bacteria.

JMT-1: a novel, spherical lytic halotolerant phage isolated from Yuncheng saline lake

ABSTRACT This work described a novel halotolerant phage, JMT-1, with a spherical morphology. JMT-1, which was isolated from a hypersaline lake, could produce clear plaques on Chromohalobacter sp. LY7-3. The purified virions are spherical, have no visible tail, and are about 30-50 nm in diameter. JMT-1 has a wide host range, and this study showed that the phage can infect at least five halophilic bacteria. The proteins of JMT-1 were analyzed using sodium dodecyl sulfate polyacrylamide gel electrophoresis, and six proteins were detected. Results show that JMT-1 is a bacteriophage with a linear double-stranded DNA. Meanwhile, the genome is approximately 23 kb in length and is sensitive to the restriction endonucleases Bam I, EcoR I, Hind III and Kpa I. JMT-1 has a high titer, approaching 1.5 × 109 pfu/mL after dilution to 10−6 pfu/mL. The phage is also sensitive to chloroform but not to temperature, pH, and lowered salt concentration. JMT-1 is a spherical lytic halotolerant phage with a wide host range and has the tolerance to specific extreme environments. These data could provide references for studying phage resources in extreme environments and would also provide the useful methods for isolation and identification of other valuable phage in the salt lake environment.

An experimental study of phage mediated bactericidal selection & emergence of the El Tor Vibrio cholerae.

Background & objectives: Factor causing the elimination of the classical biotype of Vibrio cholerae O1, and its replacement by the El Tor biotype causing the 7th cholera pandemic are unclear. Possible ability of the El Tor strains to adapt better than the classical strains to undefined environmental forces have been largely implicated for the change. Here we describe an environmental bacteriophage designated JSF9 which might have contributed to the range of factors. Methods: Competition assays were conducted in the infant mice model and in microcosms between representative El Tor and classical biotype strains in the absence or in the presence of JSF9 phage. Results: The JSF9 phage was found to kill classical strains and favour enrichment of El Tor strains, when mixtures containing strains of the two biotypes and JSF9 phage were subjected to alternate passage in infant mice and in samples of environmental water. Spontaneous derivatives of the classical biotype strains, as well as transposon mutants which developed resistance to JSF9 phage were found to be defective in colonization in the infant mouse model. Interpretation & conclusions: These results suggest that in addition to other factors, the inherent ability of El Tor biotype strains to evade predation by JSF9 or similar phages which kill classical biotype strains, might have enhanced the emergence of El Tor strains as the predominant pandemic biotype.

Molecular mechanism of acquisition of the cholera toxin genes.

One of the major pathogenic determinants of Vibrio cholerae, the cholera toxin, is encoded in the genome of a filamentous phage, CTX. CTX makes use of the chromosome dimer resolution system of V. cholerae to integrate its single stranded genome into one, the other, or both V. cholerae chromosomes. Here, we review current knowledge about this smart integration process.

Can painting human cells with exogenous maltoporin enable efficient therapeutic gene transfer by bacteriophage lambda vectors? / Las células humanas marcadas con maltoporinas exógenas, ¿permiten una terapia eficiente de tranferencia de genes por vectores bacteriofagos lambda?

Many gene therapy strategies require transfer of high-molecular weight DNA into human cells. To enable clinical trials, these vectors need to be produced on a large scale and at low cost. The production of effective high-capacity vectors like HSV-amplicons and helper-dependent adenoviral vectors is difficult to up-scale, so new inexpensive vectors are needed for the efficient delivery of high-molecular weight DNA to human cells. Bacteriophage lambda vectors can accommodate up to about 46 kb of therapeutic DNA and can be easily produced in an industrial setting. However, the lambda vectors transfer DNA into mammalian cells with only a low efficiency. It was shown that bacteriophage lambda virions ejected their DNA in the presence of the purified receptor for bacteriophage lambda, maltoporin (LamB protein), encoded by the malB gene of Shigella sonnei 3070. This property of S. sonnei maltoporin was exploited for the bacteriophage injection-driven DNA loading of liposomes and other polymer nanocontainers displaying maltoporin. Relying on the above evidence I hypothesize that the efficient gene transfer by industrially produced bacteriophage lambda vector virions, such as cosmid transducing particles, to human cells can be accomplished after incorporation (protein painting) of the purified S. sonnei maltoporin into the human plasma membrane.

Optimization of Streptomyces bacteriophage phiC31 integrase system to prevent post integrative gene silencing in pulmonary type II cells

phiC31 integrase has emerged as a potent tool for achieving long-term gene expression in different tissues. The present study aimed at optimizing elements of phiC31 integrase system for alveolar type II cells. Luciferase and beta-galactosidase activities were measured at different time points post transfection. 5-Aza-2'deoxycytidine (AZA) and trichostatin A (TSA) were used to inhibit DNA methyltransferase and histone deacetylase complex (HDAC) respectively. In A549 cells, expression of the integrase using a CMV promoter resulted in highest integrase activity, whereas in MLE12 cells, both CAG and CMV promoter were equally effective. Effect of polyA site was observed only in A549 cells, where replacement of SV40 polyA by bovine growth hormone (BGH) polyA site resulted in an enhancement of integrase activity. Addition of a C-terminal SV40 nuclear localization signal (NLS) did not result in any significant increase in integrase activity. Long-term expression studies with AZA and TSA, provided evidence for post-integrative gene silencing. In MLE12 cells, both DNA methylases and HDACs played a significant role in silencing, whereas in A549 cells, it could be attributed majorly to HDAC activity. Donor plasmids comprising cellular promoters ubiquitin B (UBB), ubiquitin C (UCC) and elongation factor 1alpha (EF1alpha) in an improved backbone prevented post-integrative gene silencing. In contrast to A549 and MLE12 cells, no silencing could be observed in human bronchial epithelial cells, BEAS-2B. Donor plasmid coding for murine erythropoietin under the EF1alpha promoter when combined with phiC31 integrase resulted in higher long-term erythropoietin expression and subsequently higher hematocrit levels in mice after intravenous delivery to the lungs. These results provide evidence for cell specific post integrative gene silencing with phiC31 integrase and demonstrate the pivotal role of donor plasmid in long-term expression attained with this system.

Bacteriophages and insertion sequences of Chromobacterium violaceum ATCC 12472

A fluid genome is a great advantage to prokaryotes, enabling quick adaptation to various types of ecological niches and to diverse environmental selective pressures. A substantial portion of these sudden changes is mediated by lateral gene transfer (LGT), through genetic recombination mechanisms, such as transformation, conjugation and transduction. The recent sequencing of several organisms has offered a new approach to the study of LGT, using comparison and analysis of nucleotide sequences dispersed throughout the genome of these species. This analysis in Choromobacterium violaceum has revealed four prophage and 12 insertion sequences, suggesting genetic exchange with several other bacterial species, including Salmonella enterica, Ralstonia and Xanthomonas. An Rhs (recombination hot spot) element (containing a vgr-like gene) was also observed, the function of which remains unknown, but it has a sequence related to species of Acinetobacter and Sphingomonas. These results support the role of LGT in the acquisition of new traits by C. violaceum

Construction and significance of directional expression cDNA library from human NB4 cells / 华中科技大学学报（医学）（英德文版）

Human acute premyeloid leukemia cell cDNA expression library was constructed to screen acute premyeloid leukemia tumor antigen. Total RNA and purified mRNA were extracted from human premyeloid cell line NB4. First and second strands of cDNA were synthesized by reverse transcription. After blunting, the cDNA fragments were ligated with EcoR I adapters. Then the cDNAs were digested with Xho I, and less than 400 bp cDNA fragment was removed by Sephacryl-S400 spin column, the remaining were ligated with lambdaZAP vector. The recombinants were packaged in vitro, and a small portion of packaged phage was used to infect E. coli XL1-Blue-MRF' for titration. The recombinants were examined by color selection. In order to evaluate the size of cDNA inserts and the diversity of library, the pBK-CMV phagemid was excised from the ZAP express vector by using ExAssist helper phage with XLOLR strain, and then the pBK-CMV phagemid was digested by Xho I and EcoR I. The results showed that the NB4 cell line cDNA library consisting of 1.65 x 10(6) recombinant bacteriophages was constructed with the recombinant ratio of 99.6%. The average length of the recombinant exogenous inserts was about 1.7 kb. It was concluded that the constructed cDNA library are deserved to screen target clones.

A prospective study of phage types & biotypes of Salmonella enterica serotype Typhi isolated from hospitalized children in Kolkata, India.

BACKGROUND & OBJECTIVES: Kolkata and its suburbs in eastern India faced an epidemic of typhoid fever in 1990. A prospective, hospital and laboratory based study over a period of 12 yr (1990-2001), on the phage typing and biotyping pattern of Salmonella enterica serotype Typhi was carried out, to see if there has been a change. METHODS: A total of 338 S. enterica serotype Typhi isolates from 1491 blood samples were phage typed and biotyped. The mean age of isolation was calculated. RESULTS: The age distribution of subjects (neonates to 12 yr) has been analysed. Of the 338 (22.7%) isolates obtained, eight different S. enterica serotype Typhi phage types were detected. Biotype I (95.8%) was more prevalent as compared to biotype II (4.1%). Phage type E1 was the commonest phage type in Kolkata and its suburbs. INTERPRETATION & CONCLUSION: The mean age at isolation was found to be 6.7 +/- 3.3 yr. Biotype I was predominant and it was of interest that all strains of phage type E1 belonged to biotype I.

Estudo da proteína de choque térmico GRP788 para o desenvolvimento de um sistema de receptor-ligante para o câncer de próstata / The use of the heat-shock protein GRP78 for the development of a receptor-ligant ssystem in prostate cancer

Terapêuticas mais eficazes são necessárias para o câncer de próstata avançado. A Proteína regulada pela glicose-78 (GRP78) foi recentemente descrita como sendo um possível marcador molecular para a doença. Neste estudo, avaliou-se a GRP78 no desenvolvimento de um sistema de receptor-ligante para o câncer de próstata. Inicialmente, foram criados dois fagos com afinidade à GRP78 e foi demonstrado que ambos se ligam especificamente à proteína in vitro e em células de câncer de próstata. Em seguida, mostrou-se que ambos os fagos com afinidade à GRP78 rastrearam xeno-tumores prostáticos in vivo, e finalmente mostrou-se que os fagos ligam-se especificamente à GRP78 em metástases ósseas de câncer de próstata humano /Improved therapies are needed for advanced prostate cancer. The Glucose-regulated protein-78 (GRP78) was recently described as molecular marker for prostate cancer. We hipothesized that GRP78 could be used in the development of a receptor-ligand system. We initially cloned two GRP78-targeting plasmids (WIFPWIQL and WDLAWMFRLPVG) into a fUSE5-based phage. We showed that both phage bound specifically to GRP78 in vitro and to intact prostate cancer cells, and was internalized by those cells. GRP78-binding phage showed a strong homing in vivo to human prostate cancer xenografts. Finally, we showed that both phage bound specifically to GRP78 expressed in human prostate cancer bone metastases...

Genetically engineered single-chain Fvs of human immunoglobulin against hepatitis C virus nucleocapsid protein derived from universal phage display library.

Specific single-chain Fvs (scFvs) of human immunoglobulin that specifically recognized the recombinant hepatitis C virus (HCV) nucleocapsid protein were isolated from a large phage display antibody library. This universal library of genetically engineered filamentous phagemids displayed random pairings of the variable regions of both human heavy and light chain immunoglobulin in the scFv format. Specific clones were isolated by affinity selection with purified recombinant HCV protein fused to glutathione-S-transferase (GST). The GST-specific clones were excluded by blocking the phagemid library with GST prior to the selection. After 4 rounds of selection, the HCV-reactive clones were enriched by a factor of 100,000. About 4% and 9% of the clones from rounds 4 and 5, respectively, specifically reacted to the HCV portion of the fusion protein in an enzyme immunoassay. The specificity was confirmed by specific binding inhibition with plasma from an HCV-infected individual. Nucleotide sequence analysis of 3 HCV-specific clones indicated that all 3 clones contained an almost identical VH gene sequence which was derived from the VH3 germline gene family. These clones had different VL gene sequences of the lambda type. There were some differences between nucleotide and amino acid sequences of the HCV-specific scFv genes and those of the closest matched germline genes, indicating the presence of somatic mutation. This study illustrated the feasibility of using antibody engineering technology with the universal phage display library to isolate human antibodies with predefined specificity to important microbial pathogen which may be useful for future therapeutic purpose.