The horizontal genetic transfer (HGT) of antibiotic resistance genes (ARGs) mediated by species-specific bacteriophages contributes to the emergence of antibiotic-resistant strains in natural ...populations of human and animal bacterial pathogens posing a significant threat to global public health. However, it is unclear and needs to be determined whether polyvalent bacteriophages play any role in the intergeneric transmission of ARGs. In this study, we examined the genome sequences of 2239 bacteriophages from different sources for the presence of ARGs. The identified ARG-carrying bacteriophages were then analyzed by PHACTS, PHAST, and HostPhinder programs to determine their lifestyles, genes coding for bacterial cell lysis, recombinases, and a spectrum of their potential host species, respectively. We employed the SplitsTree, RDP4 and SimPlot software packages in recombination tests to identify HGT events of ARGs between these bacteriophages and bacteria. In our analyses, some ARG-carrying bacteriophages exhibited temperate and/or polyvalent patterns. The bootstrap values (97–100) for the SplitsTree-generated parallelograms, fit values (97–100) for splits networks, Phi
P
values (< 10
−17
to 3.9 × 10
−16
), RDP4
P
values (≤ 7.8 × 10
−03
), and the SimPlot results, provided strong statistical evidence for the phage transduction events of
bla
CTX-M
,
mel
, and
tetM
loci on inter-species level. These events involved several host species such as
Escherichia coli, Salmonella enterica, Shigella sonnei, Streptococcus pneumoniae
and
Bacillus coagulans.
HGT of
mel
loci between
Erysipelothrix
and
Streptococcus
phages were also detected. These results firmly suggest that certain bacteriophages possibly with temperate properties induce the intergeneric dissemination of
bla
CTX-M
,
mel
and
tetM
in the above species.
During field surveys conducted from July to October 2018–2020 in the eastern part of Georgia (Caucasus region), 145 out of 8000 (1.8%) and 147 out of 6600 (2.2%) grapevine plants, respectively, from ...mother stock/collection fields and commercial vineyards, were found exhibiting typical or suspicious grapevine yellows (GY) symptoms. Most of the symptomatic grapevine plants of Georgian cultivars showed mild symptoms with no berry alterations. Leaf samples from symptomatic plants were analyzed by serological (DAS- -ELISA) and molecular (two previously published protocols of TaqMan triplex real-time PCR, here named Set I and Set II) tools for detecting GY-associated phytoplasmas. The presence of GY phytoplasmas was not detected in any examined grapevines by a serological method. GY phytoplasmas were identified in 22.41% and 6.9% symptomatic plants from mother stock and collection vineyards and in 48.3 and 19.0% symptomatic plants from commercial vineyards by Set I and Set II PCRs, respectively. As expected from previous studies reporting the wide presence of bois noir (BN) in Georgian vineyards, ‘Candidatus Phytoplasma solani’(CaPsol) was detected in most phytoplasma-infected plants (47.6%), with the highest infection rate in Chardonnay. Phytoplasmas belonging to taxonomic group 16SrV were detected in 45.6% of the phytoplasma-infected grapevines. To the best of our knowledge, this is the first report of 16SrV phytoplasmas in Georgia and in the Caucasus region. Further molecular typing of 16SrV phytoplasma strains is necessary to determine if such strains are associated with flavescence dorée (FD). The knowledge of typical GY symptoms and the utilization of accurate diagnostic tools are crucial for preventing pathogen spread and producing healthy planting material. Based on the results obtained in this study, the presence of BN and 16SrV phytoplasmas should be monitored in the next years using triplex real-time PCR.
In 2014, the National Wine Agency of the Republic of Georgia initiated a three-year “Research Project for the study of Georgian Grapes and Wine Culture. Through collaborative research by Georgian and ...foreign institutions and researchers, the project aims to: stimulate research of Georgian viticulture and viniculture, through the lens of the country with the earliest tradition of grape domestication and winemaking; and to reconstruct the continuous development of viticulture and wine culture through time. The project advances the study of grape and wine culture by utilizing a multidisciplinary approach, including: archaeology, history, ethnography, molecular genetics, biomolecular archaeology, palaeobotany, ampelography, enology, climatology and other scientific fields. These studies are diachronic in their approach, beginning with the oldest Neolithic civilizations, to present day, creating a holistic understanding of the continuity and complexity of Georgian Wine Culture to help popularize Georgian Wine throughout the global wine market.
Aims: The chloroplast DNA sequence of eight Georgian grape cultivars (Rkatsiteli, Saperavi, Meskhuri Mtsvane, Chkhaveri, Aladasturi, Krakhuna, Tsitska, Tsolikouri) and three French cultivars ...(Chardonnay, Gouais Blanc, Chasselas), belonging to four different haplogroups (AAA, ATT, ATA, GTA), was determined by Illumina resequencing of genomic DNA. The chloroplast DNA sequence of the Maxxa cultivar was used as reference. Methods and results: The comparison of sequenced chloroplast DNA gave 100 % identity to Chardonnay and Gouais Blanc, differing from Meskhuri Mtsvane by two insertions/deletions (indels) (all ATA haplogroup). The difference between Chasselas and Saperavi was a single insertion (both ATT haplogroup), while Maxxa, Chkhaveri, Aladasturi, Krakhuna, Tsitska and Tsolikouri were all identical (all members of the GTA haplogroup). Forty-seven identical single nucleotide polymorphisms (SNPs) were detected in the AAA, ATA and ATT haplogroups in comparison to the reference DNA. Additionally, 18 SNPs were detected for the ATT haplogroup, 4 for AAA, 6 for ATA and 11 for both AAA and ATA. The phylogenetic results show that the ATT, AAA and ATA haplogroups are more closely related to each other than to the GTA haplogroup. Conclusion: In the sequencing data of grape genomic DNA at the coverage (read depth) of chromosomal DNA 30-40, the coverage of chloroplast DNA reaches several thousand reads per bp due to the high number of chloroplast DNA copies in genomic DNA, much higher than necessary for resequencing. Based on these data, a new methodology of simultaneous resequencing of large number of chloroplast DNA was developed without preliminary chloroplast isolation or chloroplast enrichment. Significance and impact of the study: This method has great potential for expanding both phylogenetic and population genetic information on the evolution of domesticated crops.
We elucidate grapevine evolution and domestication histories with 3525 cultivated and wild accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape ecotypes caused ...by continuous habitat fragmentation. Then, domestication occurred concurrently about 11,000 years ago in Western Asia and the Caucasus to yield table and wine grapevines. The Western Asia domesticates dispersed into Europe with early farmers, introgressed with ancient wild western ecotypes, and subsequently diversified along human migration trails into muscat and unique western wine grape ancestries by the late Neolithic. Analyses of domestication traits also reveal new insights into selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These data demonstrate the role of the grapevines in the early inception of agriculture across Eurasia.
The horizontal genetic transfer (HGT) of antibiotic resistance genes (ARGs) mediated by species-specific bacteriophages contributes to the emergence of antibiotic-resistant strains in natural ...populations of human and animal bacterial pathogens posing a significant threat to global public health. However, it is unclear and needs to be determined whether polyvalent bacteriophages play any role in the intergeneric transmission of ARGs. In this study, we examined the genome sequences of 2239 bacteriophages from different sources for the presence of ARGs. The identified ARG-carrying bacteriophages were then analyzed by PHACTS, PHAST, and HostPhinder programs to determine their lifestyles, genes coding for bacterial cell lysis, recombinases, and a spectrum of their potential host species, respectively. We employed the SplitsTree, RDP4 and SimPlot software packages in recombination tests to identify HGT events of ARGs between these bacteriophages and bacteria. In our analyses, some ARG-carrying bacteriophages exhibited temperate and/or polyvalent patterns. The bootstrap values (97-100) for the SplitsTree-generated parallelograms, fit values (97-100) for splits networks, Phi P values (< 10
to 3.9 × 10
), RDP4 P values (≤ 7.8 × 10
), and the SimPlot results, provided strong statistical evidence for the phage transduction events of bla
, mel, and tetM loci on inter-species level. These events involved several host species such as Escherichia coli, Salmonella enterica, Shigella sonnei, Streptococcus pneumoniae and Bacillus coagulans. HGT of mel loci between Erysipelothrix and Streptococcus phages were also detected. These results firmly suggest that certain bacteriophages possibly with temperate properties induce the intergeneric dissemination of bla
, mel and tetM in the above species.
The EU's European Neighbourhood Policy (ENP) promotes stability, security and prosperity in neighbouring countries. It builds on common interests and a shared commitment to cooperate on key priority ...areas including food safety. This technical report presents a summary of an online workshop held on 4 November 2020, with East European Neighbourhood (ENP‐East) countries and contributions from the World Health Organization (WHO), the European Commission (DG SANTE and DG‐NEAR), the German Federal Institute for Risk Assessment (Bundesinstitut für Risikobewertung, BfR) and the Institute of Food safety, Animal Health and Environment "BIOR" of Latvia.The aim of the workshop was to present the current status of risk assessment activities in the six ENP‐East countries (Armenia, Azerbaijan, Belarus, Georgia, Moldova and Ukraine), discuss the challenges they face and explore opportunities for cooperation with the European Union (EU) and other international organisations. A summary of the presentations is provided along with relevant key risk assessment activities in each country. Contributions from EFSA and the WHO are also included. Opportunities and challenges for the food safety area are discussed particularly to further enhance risk assessment capabilities in ENP countries through cooperation, capacity building and staff exchange between ENP, EU and international organisations as the most efficient tools to achieve such goals.
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