Complete Genome Sequence Data of Nonpathogenic Strain Rhizobium vitis VAR03-1, a Biological Control Agent for Grapevine Crown Gall Disease

Crown gall disease in grapevine is caused by pathogenic strains of Rhizobium vitis with a tumor-inducing (Ti) plasmids. A nonpathogenic strain, VAR03-1 of R. vitis, has been isolated from the grapevine root of nursery stock and it was shown to act as a biological control agent to crown gall disease. Its disease-suppressive effect was observed even when it was coinoculated with the pathogen in a 1:1 ratio. Here, we present the complete genome data of R. vitis VAR03-1, assembled by sequencing reads obtained by both PacBio and Illumina technologies with annotation. This genome sequence could contribute to investigations of the molecular basis underlying the biocontrol activity as well as the root-colonization ability of this bacterial strain. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

“Burrata di Andria” PGI Cheese: Physicochemical and Microbiological Features

In the last century, the exponential increase of industrial food production led to the disappearance of “Italian traditional niche products”. However, national regulations allowed the preservation of several of these products, including the burrata cheese. Twenty-one samples from three different batches of “Burrata di Andria” Protected Geographical Indication (PGI) were purchased from dairy factories of the PGI consortium. Moisture value of PGI Burrata cheese was significantly higher than that before the PGI release. Moreover, a significantly lower NaCl value was detected in PGI raw milk Burrata cheeses with respect to non-PGI ones, while an opposite situation was detected in pasteurized milk Burrata cheeses. As for pH, in all PGI products lower values were observed with respect to non-PGI products, which resulted significant only in pasteurized ones. No Salmonella spp., Listeria monocytogenes, and Bacillus cereus were detected, while nine samples were positive for a nonpathogenic strain of Yersinia enterocolitica. Total viable count (TVC) and Escherichia coli resulted significantly lower in pasteurized than in raw milk PGI Burrata cheese samples. Although samples analyzed can be considered microbiologically safe, these were borderline and/or unsatisfactory for E. Coli and coagulase-positive staphylococci (CPS) according to process hygiene criteria established by European regulation. Therefore, different strategies should be adopted to improve products hygiene in the considered dairy factories.

Differential Expression of Fungal Genes Determines the Lifestyle of Plectosphaerella Strains During Arabidopsis thaliana Colonization

The fungal genus Plectosphaerella comprises species and strains with different lifestyles on plants, such as P. cucumerina, which has served as model for the characterization of Arabidopsis thaliana basal and nonhost resistance to necrotrophic fungi. We have sequenced, annotated, and compared the genomes and transcriptomes of three Plectosphaerella strains with different lifestyles on A. thaliana, namely, PcBMM, a natural pathogen of wild-type plants (Col-0), Pc2127, a nonpathogenic strain on Col-0 but pathogenic on the immunocompromised cyp79B2 cyp79B3 mutant, and P0831, which was isolated from a natural population of A. thaliana and is shown here to be nonpathogenic and to grow epiphytically on Col-0 and cyp79B2 cyp79B3 plants. The genomes of these Plectosphaerella strains are very similar and do not differ in the number of genes with pathogenesis-related functions, with the exception of secreted carbohydrate-active enzymes (CAZymes), which are up to five times more abundant in the pathogenic strain PcBMM. Analysis of the fungal transcriptomes in inoculated Col-0 and cyp79B2 cyp79B3 plants at initial colonization stages confirm the key role of secreted CAZymes in the necrotrophic interaction, since PcBMM expresses more genes encoding secreted CAZymes than Pc2127 and P0831. We also show that P0831 epiphytic growth on A. thaliana involves the transcription of specific repertoires of fungal genes, which might be necessary for epiphytic growth adaptation. Overall, these results suggest that in-planta expression of specific sets of fungal genes at early stages of colonization determine the diverse lifestyles and pathogenicity of Plectosphaerella strains.

The Natural Large Genomic Deletion Is Unrelated to the Increased Virulence of the Novel Genotype Fowl Adenovirus 4 Recently Emerged in China

Since 2015, severe hydropericardium-hepatitis syndrome (HHS), caused by a highly pathogenic fowl adenovirus 4 (FAdV-4), emerged in China. In our previous study, the FAdV-4 has been identified as a novel genotype with a unique 1966-bp nucleotide deletion (1966Del) between open reading frame 42 and 43. In this study, the natural 1966Del was frequently identified among 17 clinical isolates and other reported Chinese clinical strains. To investigate the relationship between 1966Del and the increased virulence of the novel FAdV-4, a CRISPR/Cas9 operating platform for FAdV-4 was developed for the first time in this study. Based on this platform, a Re1966 strain was rescued, inserted the relative 1966Del sequence of a nonpathogenic strain KR5. In the pathogenicity study, the Re1966 strain retained high virulence for specific-pathogen-free chickens, similar to the parental wild-type HLJFAd15, although the survival time of chickens infected with Re1966 was much longer. Therefore, the natural 1966Del was identified as a non-essential site for the increased virulence of the emerged novel FAdV-4. Although further research on the virulence-determining region or point within the genome of the novel FAdV-4 is needed, the CRISPR/Cas9 operating platform for the novel FAdV-4 was developed and successfully applied to edit the genomic DNA for the first time, and it provides a novel powerful tool for both basic virology studies and vaccine vector development of FAdVs.

Quantifying the Effects of Water Temperature, Soap Volume, Lather Time, and Antimicrobial Soap as Variables in the Removal of Escherichia coli ATCC 11229 from Hands

ABSTRACT The literature on hand washing, while extensive, often contains conflicting data, and key variables are only superficially studied or not studied at all. Some hand washing recommendations are made without scientific support, and agreement between recommendations is limited. The influence of key variables such as soap volume, lather time, water temperature, and product formulation on hand washing efficacy was investigated in the present study. Baseline conditions were 1 mL of a bland (nonantimicrobial) soap, a 5-s lather time, and 38°C (100°F) water temperature. A nonpathogenic strain of Escherichia coli (ATCC 11229) was the challenge microorganism. Twenty volunteers (10 men and 10 women) participated in the study, and each test condition had 20 replicates. An antimicrobial soap formulation (1% chloroxylenol) was not significantly more effective than the bland soap for removing E. coli under a variety of test conditions. Overall, the mean reduction was 1.94 log CFU (range, 1.83 to 2.10 log CFU) with the antimicrobial soap and 2.22 log CFU (range, 1.91 to 2.54 log CFU) with the bland soap. Overall, lather time significantly influenced efficacy in one scenario, in which a 0.5-log greater reduction was observed after 20 s with bland soap compared with the baseline wash (P = 0.020). Water temperature as high as 38°C (100°F) and as low as 15°C (60°F) did not have a significant effect on the reduction of bacteria during hand washing; however, the energy usage differed between these temperatures. No significant differences were observed in mean log reductions experienced by men and women (both 2.08 log CFU; P = 0.988). A large part of the variability in the data was associated with the behaviors of the volunteers. Understanding what behaviors and human factors most influence hand washing may help researchers find techniques to optimize the effectiveness of hand washing.

Origins of the current seventh cholera pandemic

Vibrio choleraehas caused seven cholera pandemics since 1817, imposing terror on much of the world, but bacterial strains are currently only available for the sixth and seventh pandemics. The El Tor biotype seventh pandemic began in 1961 in Indonesia, but did not originate directly from the classical biotype sixth-pandemic strain. Previous studies focused mainly on the spread of the seventh pandemic after 1970. Here, we analyze in unprecedented detail the origin, evolution, and transition to pandemicity of the seventh-pandemic strain. We used high-resolution comparative genomic analysis of strains collected from 1930 to 1964, covering the evolution from the first available El Tor biotype strain to the start of the seventh pandemic. We define six stages leading to the pandemic strain and reveal all key events. The seventh pandemic originated from a nonpathogenic strain in the Middle East, first observed in 1897. It subsequently underwent explosive diversification, including the spawning of the pandemic lineage. This rapid diversification suggests that, when first observed, the strain had only recently arrived in the Middle East, possibly from the Asian homeland of cholera. The lineage migrated to Makassar, Indonesia, where it gained the important virulence-associated elementsVibrioseventh pandemic island I (VSP-I), VSP-II, and El Tor type cholera toxin prophage by 1954, and it then became pandemic in 1961 after only 12 additional mutations. Our data indicate that specific niches in the Middle East and Makassar were important in generating the pandemic strain by providing gene sources and the driving forces for genetic events.

Coculture of Escherichia coli O157:H7 with a Nonpathogenic E. coli Strain Increases Toxin Production and Virulence in a Germfree Mouse Model

ABSTRACTEscherichia coliO157:H7 is a notorious foodborne pathogen due to its low infectious dose and the disease symptoms it causes, which include bloody diarrhea and severe abdominal cramps. In some cases, the disease progresses to hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS), due to the expression of one or more Shiga toxins (Stx). Isoforms of Stx, including Stx2a, are encoded within temperate prophages. In the presence of certain antibiotics, phage induction occurs, which also increases the expression of toxin genes. Additionally, increased Stx2 accumulation has been reported when O157:H7 was cocultured with phage-susceptible nonpathogenicE. coli. This study characterized anE. coliO157:H7 strain, designated PA2, that belongs to the hypervirulent clade 8 cluster. Stx2a levels after ciprofloxacin induction were lower for PA2 than for the prototypical outbreak strains Sakai and EDL933. However, during coculture with the nonpathogenic strainE. coliC600, PA2 produced Stx2a levels that were 2- to 12-fold higher than those observed during coculture with EDL933 and Sakai, respectively. Germfree mice cocolonized by PA2 and C600 showed greater kidney damage, increased Stx2a accumulation in feces, and more visible signs of disease than mice given PA2 or C600 alone. These data suggest one mechanism by which microorganisms associated with the colonic microbiota could enhance the virulence ofE. coliO157:H7, particularly a subset of clade 8 strains.

Evaluation of the Nonpathogenic Agrobacterium vitis Strain ARK-1 for Crown Gall Control in Diverse Plant Species

The nonpathogenic strain of Agrobacterium (=Rhizobium) vitis ARK-1 is a biological agent able to effectively control grapevine crown gall. In this study, treating apple, Japanese pear, peach, rose, and tomato by soaking the roots in a cell suspension of ARK-1 before planting into soil infected with tumorigenic Agrobacterium spp. reduced the number of plants developing crown gall tumors. Meta-analyses of the results from six field trials of apple, four field trials of Japanese pear, and four field trials of peach, from 2010 to 2013, showed integrated risk ratio (IRR) after treatment with ARK-1 to be 0.38 for apple crown gall, 0.16 for Japanese pear crown gall, and 0.20 for peach crown gall, indicating that the disease incidence was significantly reduced by ARK-1 treatment. Meta-analyses of the results from three greenhouse trials of rose and three greenhouse trials of tomato showed IRR after treatment with ARK-1 to be 0.29 for rose crown gall and 0.16 for tomato crown gall, indicating that the disease incidence was significantly reduced by ARK-1 treatment. These results indicated that control by ARK-1 covers five different species of host plants and tumorigenic (Ti) strains of Agrobacterium species.