Acquisition, loss, and replication of functional modules promote the genetic diversity of Salmonella bacteriophages.

Owing to the threats that Salmonella poses to public health and the abuse of antimicrobials, bacteriophage therapy against Salmonella is experiencing a resurgence. Although several phages have been reported as safe and efficient for controlling Salmonella, the genetic diversity and relatedness among Salmonella phages remain poorly understood. In this study, whole-genome sequences of 91 Salmonella bacteriophages were obtained from the National Center for Biological Information genome database. Phylogenetic analysis, mosaic structure comparisons, gene content analysis, and orthologue group clustering were performed. Phylogenetic analysis revealed four singletons and two major lineages (I-II), including five subdividing clades, of which Salmonella phages belonging to morphologically distinct families were clustered in the same clade. Chimeric structures (n = 31), holin genes (n = 18), lysin genes (n = 66), DNA packaging genes (n = 55), and DNA metabolism genes (n = 24) were present in these phages. Moreover, phages from different subdivided clusters harboured distinct genes associated with host cell lysis, DNA packaging, and DNA metabolism. Notably, phages belonging to morphologically distinct families shared common orthologue groups. Although several functional modules of phages SS1 and SE16 shared > 99% nucleotide sequence identity with phages SI2 and SI23, the major differences between these phages were the absence and replication of functional modules. The data obtained herein revealed the genetic diversity of Salmonella phages at genomic, structural, and gene content levels. The genetic diversity of Salmonella phages is likely owing to the acquisition, loss, and replication of functional modules.

Isolation and characterization of the new isolated bacteriophage YZU-L1 against Citrobacter freundii from a package-swelling of meat product.

Citrobacter freundii is an important foodborne pathogen that can cause urethritis, bacteremia, necrotizing abscess, and meningitis in infants. In this study, a gas-producing isolate from vacuum-packed meat products was identified as C. freundii by 16S rDNA. In addition, a new virulent phage YZU-L1, which could specifically lyse C. freundii, was isolated from sewage samples in Yangzhou. Transmission electron microscopy showed that phage YZU-L1 had a polyhedral head of 73.51 nm in diameter and a long tail of 161.15 nm in length. According to phylogenetic analysis employing the terminase large subunit, phage YZU-L1 belonged to the Demerecviridae family and the Markadamsvirinae subfamily. The burst size was 96 PFU/cell after 30 min of latent period and 90 min of rising period. Phage YZU-L1 could maintain high activity at pH of 4-13, and resist 50 °C for up to 60 min. The complete genome of YZU-L1 was 115,014 bp double-stranded DNA with 39.94% G + C content, encoding 164 open reading frames (ORFs), without genes encoding for virulence, antibiotic resistance, or lysogenicity. Phage YZU-L1 treatment significantly reduced the viable bacterial count of C. freundii in a sterile fish juice model, which is expected to be a natural agent for the biocontrol of C. freundii in foods.

WGS analysis of two Staphylococcus aureus bacteriophages from sewage in China provides insights into the genetic feature of highly efficient lytic phages.

The study of bacteriophages is experiencing a resurgence with the increasing development of antimicrobial resistance in Staphylococcus aureus. Nonetheless, the genetic features of highly efficient lytic S. aureus phage remain to be explored. In this study, two lytic S. aureus phages, SapYZU11 and SapYZU15, were isolated from sewage samples from Yangzhou, China. The phage morphology, one-step growth, host spectrum and lytic activity of these phages were examined, and their whole-genome sequences were analysed and compared with 280 published genomes of staphylococcal phages. The structural organisation and genetic contents of SapYZU11 and SapYZU15 were investigated. The Podoviridae phage SapYZU11 and Herelleviridae phage SapYZU15 effectively lysed all of the 53 S. aureus strains isolated from various sources. However, SapYZU15 exhibited a shorter latent period, larger burst size and stronger bactericidal ability with an anti-bacterial rate of approximately 99.9999% for 24 h. Phylogenetic analysis revealed that Herelleviridae phages formed the most ancestral clades and the S. aureus Podoviridae phages were clustered in the staphylococcal Siphoviridae phage clade. Moreover, phages in different morphology families contain distinct types of genes associated with host cell lysis, DNA packaging and lysogeny. Notably, SapYZU15 harboured 13 DNA metabolism-related genes, 5 lysin genes, 1 holin gene and 1 DNA packaging gene. The data suggest that S. aureus Podoviridae and Siphoviridae phages originated from staphylococcal Herelleviridae phages, and the module exchange of S. aureus phages occurred in the same morphology family. Moreover, the extraordinary lytic capacity of SapYZU15 was likely due to the presence of specific genes associated with DNA replication, DNA packaging and the lytic cycle.

An ultrasensitive bacterial imprinted electrochemical sensor for the determination of Lactobacillus rhamnosus GG.

An ultrasensitive label-free electrochemical sensor based on a homemade imprinted polypyrrole (PPy) polymer film was prepared to achieve quantitative determination of Lactobacillus rhamnosus GG (LGG). The LGG-imprinted polymer (LIP) film was deposited on a portable screen-printed electrode (SPE) via electropolymerization, which constituted an independent integrated system. The main preparation parameters of the LIP sensor were investigated to obtain optimal performance. Under optimized conditions, the peak current response of the LIP sensor showed a linear relationship with the logarithmic value of LGG concentration in the range from 101 to 109 CFU mL-1 and a detection limit of 5 CFU mL-1. The proposed LIP sensor has achieved efficient, ultrasensitive, highly selective, and cost-effective detection of LGG and can be further developed for practical applications in the quality inspection and development of probiotic products.

Isolation and genomic characterization of Vmp-1 using Vibrio mimicus as the host: A novel virulent bacteriophage capable of cross-species lysis against three Vibrio spp.

Vibrio mimicus is a zoonotic pathogen that is widely distributed in aquatic habitats/environments (marine coastal water, estuaries, etc). The development of biocontrol agents for V. mimicus is imperative for the prevention and control of aquatic animal diseases and human food-borne infections. In this study, a broad-spectrum bacteriophage Vmp-1 was isolated from dealt aquatic product in a local market by double-layer agar plate method using V. mimicus CICC21613 as the host bacteria. Results indicated that Vmp-1, which belongs to the family Podoviridae, showed good pH tolerance (pH 3.0-12.0) and thermal stability (30-50 °C). The optimal multiplicity of infection (MOI) of Vmp-1 was 0.001 for a 20-min incubation and 100-min lysis period. Vmp-1 effectively controlled V. mimicus CICC21613 in LBS model (MOI = 0.0001, 0.001, 0.01, 0.1, 1) within 8 h. The full length of the Vmp-1 genome was 43,312 bp, with average GC content of 49.5%, and a total of 44 protein-coding regions. This study provides a novel phage strain that has the highest homology with vB_VpP_HA5 (GenBank: OK585159.1, 95.96%) for the development of biocontrol agents for V. mimicus.

Isolation and Characterization of a Virulent Bacteriophage for Controlling Salmonella Enteritidis Growth in Ready-to-Eat Mixed-Ingredient Salads.

ABSTRACT: Ready-to-eat vegetable salads have gained popularity worldwide. However, the microbial safety of these salads is a health concern, primarily due to Salmonella Enteritidis contamination during the growing, harvesting, processing, and handling of produce. In this study, a bacteriophage-based strategy was developed to control Salmonella Enteritidis growth in mixed-ingredient salads. The lytic Salmonella-specific phage SapYZU01 was isolated from a soil sample from a suburban vegetable field in Yangzhou (People's Republic of China). SapYZU01 has a short latent period, a large burst size, and a lytic effect against 13 Salmonella Enteritidis strains isolated from various sources (human samples, pork, deli foods, chickens, and chicken meat). The SapYZU01 genome did not contain virulence or antibiotic resistance genes. SapYZU01 significantly decreased the viability of Salmonella Enteritidis cells in iceberg lettuce, chicken meat, and mixed-ingredient (lettuce plus chicken) salads at 37 and 25°C. Bacterial levels in the salad decreased significantly (by 4.0 log CFU/g) at 25°C after treatment of contaminated lettuce before salad preparation with SapYZU01 at a multiplicity of infection (MOI) of 100. Bacterial levels were decreased by 3.8 log CFU/g at 25°C in lettuce plus chicken salads treated after the salad preparation with SapYZU01 at an MOI of 100. In contrast, treating cooked chicken meat with SapYZU01 at an MOI of 100 before mixing it with contaminated lettuce decreased the bacterial level of the salad by 1.2 log CFU/g at 25°C. These findings indicate the potential application of SapYZU01 as a natural biocontrol agent against Salmonella Enteritidis in mixed-ingredient salads. However, both the treatment method and the bacteriophage MOI must be considered when using this lytic bacteriophage in mixed-ingredient salads.

Isolation and genomic characterization of P.A-5, a novel virulent bacteriophage against Enterobacter hormaechei.

Enterobacter hormaechei is a foodborne pathogen responsible for neonatal sepsis in humans and respiratory disease in animals. In this work, a new virulent phage (P.A-5) infecting E. hormaechei was isolated from domestic sewage samples and characterized. Transmission electron microscopy revealed that P.A-5 belonged to the family Myoviridae having a head size of 77.53 nm and a tail length of 72.24 nm. The burst size was 262 PFU/cell after a latent period of 20 min. Phage P.A-5 was able to survive in a pH range of 4-9 and resist temperatures up to 55 °C for 60 min. The genome sequence of P.A-5 had homology most similar to that of Shigellae phage MK-13 (GenBank: MK509462.1). Pork artificially contaminated with E. hormaechei was used as a model to evaluate the potential of P.A-5. The results clearly showed that P.A-5 treatment can completely inhibit E. hormaechei growth in pork within 8 h, indicating the potential use of P.A-5 as a biocontrol agent for E. hormaechei.

Quantitative index imaging of coculture cells by scanning focused refractive index microscopy.

We report the quantitative refractive index (RI) imaging of cocultured cells in their living environment by scanning focused refractive index microscopy (SFRIM). Mouse microglial cells and synovial cells are cocultured on the top surface of a trapezoid prism. The RI imaging of living cells is obtained in a reflection-type method. The RI information is deduced with the simple derivative total internal reflection method, where a complex retrieval algorithm or reconstruction process is unnecessary. The outline of each cell is determined according to the RI value compared with that of the immersion liquid. The cocultured cells can be discriminated in the RI image. The measurement is nondestructive and label-free. The experimental results prove that SFRIM is a promising tool in the field of biological optics.

Measurement of complex refractive index of turbid media by scanning focused refractive index.

We present the application of scanning focused refractive index microscopy in the complex refractive index measurement of turbid media. An extra standard scattering layer is placed in front of the detector to perform scattering transformation on the reflected light. The principle of the scattering transformation is elaborated theoretically. The influence of the sample scattering is deeply and effectively suppressed experimentally. As a proof of the feasibility and accuracy of the proposed method, we demonstrate experimental data of 20% and 30% Intralipid solutions that are commonly used as phantom media for light propagation studies.

Tunable optofluidic microring laser based on a tapered hollow core microstructured optical fiber.

A tunable optofluidic microring dye laser within a tapered hollow core microstructured optical fiber was demonstrated. The fiber core was filled with a microfluidic gain medium plug and axially pumped by a nanosecond pulse laser at 532 nm. Strong radial emission and low-threshold lasing (16 nJ/pulse) were achieved. Lasing was achieved around the surface of the microfluidic plug. Laser emission was tuned by changing the liquid surface location along the tapered fiber. The possibility of developing a tunable laser within the tapered simplified hollow core microstructured optical fiber presents opportunities for developing liquid surface position sensors and biomedical analysis.

Scanning focused refractive-index microscopy.

We present a novel scanning focused refractive-index microscopy (SFRIM) technique to obtain the refractive index (RI) profiles of objects. The method uses a focused laser as the light source, and combines the derivative total reflection method (DTRM), projection magnification, and scanning technique together. SFRIM is able to determine RIs with an accuracy of 0.002, and the central spatial resolution achieved is 1 µm, which is smaller than the size of the focal spot. The results of measurements carried out on cedar oil and a gradient-refractive-index (GRIN) lens agree well with theoretical expectations, verifying the accuracy of SFRIM. Furthermore, using SFRIM, to the best of our knowledge we have extracted for the first time the RI profile of a periodically modulated photosensitive gelatin sample. SFRIM is the first RI profile-resolved reflected light microscopy technique that can be applied to scattering and absorbing samples. SFRIM enables the possibility of performing RI profile measurements in a variety of applications, including optical waveguides, photosensitive materials and devices, photorefractive effect studies, and RI imaging in biomedical fields.

Effect of tissue fluid on accurate determination of the complex refractive index of animal tissue.

We investigate the effect of tissue fluid on the measurement of complex refractive index (RI) of animal tissue. A new model is proposed and verified through experimental results of simulation samples made of glycerol and methyl-red-doped poly(methyl methacrylate). Coupled with polarized optical reflectance measurements performed on several kinds of animal muscle tissues, RIs were resolved using the new model. We find that the tissue fluid existing at the prism-sample interface is unavoidable. We also find that with a change of proportion of the tissue fluid, the RI of muscle tissue can still be measured using the new model.

Measurement of the complex refractive index of tissue-mimicking phantoms and biotissue by extended differential total reflection method.

Refractive index of biotissue is a useful optical parameter in the biomedical field. An extended differential total reflection method is introduced to determine the complex refractive index. The real part is directly determined by differential of the reflectance curve, and the imaginary part is obtained from nonlinear fitting. The method is verified by a series of tissue-mimicking phantoms, porcine muscle and porcine adipose.

Discriminating thermal effect in nonlinear-ellipse-rotation-modified Z-scan measurements.

We report that a modified Z-scan method by nonlinear ellipse rotation (NER) can be used to discriminate true nonlinear refraction from thermal effect in the transient regime and steady state. The combination of Z-scan and NER allows us to measure the third-order nonlinear susceptibility component without the influence of thermal-optical nonlinearity. The experimental results of pure CS(2) and CS(2) solutions of nigrosine verify that the transient thermal effect can be successfully eliminated from the NER-modified Z-scan measurements. This method is also extended to the case in which thermal-optical nonlinearities depend on a high repetition rate of femtosecond laser pulses for the N,N-dimethylmethanamide solutions of graphene oxide.

Analysis on the origin of the ultrafast optical nonlinearity of carbon disulfide around 800 nm.

The femtosecond open-aperture Z-scan of standard sample CS(2) at 800 and 780 nm is present here by using thinner sample length and an integrating sphere. The open-aperture Z-scan signal is verified to arise mainly from nonlinear scattering, not from two- or three-photon absorption as reported in literature. And the two- and three-photon absorption coefficients of CS(2) are negligible. Therefore, around 800 nm the femtosecond open-aperture Z-scan of CS(2) cannot be used to calibrate Z-scan measurement system, but the closed-aperture Z-scan is capable.

Polarization dependence and independence of near-field enhancement through a subwavelength circle hole.

By setting a metal rod or tooth-type structures in a single subwavelength hole, its near-field can be strongly enhanced. The near-field enhancement has strong polarization dependence when the structure in hole is twofold symmetric. Only the polarization along the longitudinal side of the metal rod or tooth-type structure can lead to strongest enhancement, which is attributed to the resonance of the localized surface plasmon. However, if the structure in hole is fourfold symmetric, the near-field enhancement is free from the polarization.

Polarization dependence of Z-scan measurement: theory and experiment.

Here we report on an extension of common Z-scan method to arbitrary polarized incidence light for measurements of anisotropic third-order nonlinear susceptibility in isotropic medium. The normalized transmittance formulas of closed-aperture Z-scan are obtained for linearly, elliptically and circularly polarized incidence beam. The theoretical analysis is examined experimentally by studying third-order nonlinear susceptibility of CS2 liquid. Results show that the elliptically polarized light Z-scan method can be used to measure simultaneously the two third-order nonlinear susceptibility components chi(3)(xyyx) and chi(3)(xxyy). Furthermore, the elliptically polarized light Z-scan measurements of large nonlinear phase shift are also analyzed theoretically and experimentally.

Evolutions of polarization and nonlinearities in an isotropic nonlinear medium.

The evolutions of polarization and nonlinearities in an isotropic medium induced by anisotropy of third-order nonlinear susceptibility were studied experimentally and theoretically. The anisotropy of imaginary part of third-order susceptibility was verified to exist by the change of ellipticity of polarization ellipse in the isotropic nonlinear medium CS(2). The changes of nonlinear refraction and nonlinear absorption depending upon the ellipticity of polarization ellipse are also presented. The numerical simulations based on two coupled nonlinear Schrödinger equations (NLSE) provide an excellent quantitative agreement with experimental results.

Nonlinear ellipse rotation modified Z-scan measurements of third-order nonlinear susceptibility tensor.

We present a method that combines the Z-scan technique with nonlinear ellipse rotation (NER) to measure third-order nonlinear susceptibility components. The experimental details are demonstrated, and a comprehensive theoretical analysis is given. The validity of this method is verified by the measurements of the nonlinear susceptibility tensor of a well-characterized liquid, CS2.

[A high sensitivity optical multichannel analyzer].

Noise sources of the CCD as the photoelectric detection device in an optical multichannel analyzer (OMA) were analyzed, and noise suppression methods were discussed. A high sensitivity OMA was developed successfully on the basis of the noise suppression techniques, and the 7th spectral lines of Balmer series of hydrogen and deuterium were resolved clearly by the OMA. Its sensitivity was enhanced by one order of magnitude, compared with those reported in the literatures. This OMA also showed high resolution, high precision and good reliability in the authors' experiments.