As the causal agent of the grapevine yellows disease Bois noir, '
Phytoplasma solani' has a major economic impact on grapevines. To improve the control of Bois noir, it is critical to understand the ...very complex epidemiological cycles that involve the multiple "
. P. solani" host plants and insect vectors, of which
is the most important. In the present study, multiple genotyping of the
,
, and
genes was performed. This involved archived grapevine samples that were collected during an official survey of grapevine yellows throughout the wine-growing regions of Slovenia (from 2003 to 2016), plus samples from Austrian grapevines, stinging nettle, field bindweed, and insect samples (collected from 2012 to 2019). The data show that the tuf-b2 type of the
gene has been present in eastern Slovenia since at least 2003. The hypotheses that the occurrence of the haplotypes varies due to the geographical position of Slovenia on the Italian-Slovenian Karst divide and that the haplotypes are similar between Slovenian and Austrian Styria were confirmed. The data also show haplotype changes for host plants and
.
associated with '
. P. solani,' which might be linked to new epidemiological cycles of this phytoplasma that involve not just new plant sources and new insect vectors, but also climate and land-use changes.
Lactococcosis is a bacterial infection that is characterized by the appearance of septicemia in fish. Traditionally, the identification of causes of disease outbreaks in aquaculture poses a major ...challenge due to their comparable characteristics. In this study, simple PCR and sequencing based on the tuf gene were developed to identify isolates belonging to the Streptococcaceae family. The outbreaks of lactococcosis in rainbow trout have been mainly associated with Lactococcus garvieae, but the emergence of closely related species, Lactococcus petauri and Lactococcus formosensis pose a challenge in accurate identification. The study aimed to identify Gram-positive catalase-negative cocci and differentiate between Lactococcosis-causing bacteria (LCB) in rainbow trout isolates associated with lactococcosis outbreaks in Iran. Seventy-five Gram-positive cocci strains from diseased rainbow trout were tested using a PCR and sequencing method targeting the tuf gene. Sequence and phylogenetic analyses were conducted to distinguish between closely related Lactococcus species. The PCR results revealed a successful amplification with tuf gene primers for all strains, allowing species identification. The sequence analysis showed that all 29 isolates initially identified as L.garvieae were 100% identical to L.petauri, indicating a previous misclassification. This work is the first report by L.petauri of Iran. Analysis of tuf gene sequences revealed different patterns of single nucleotide polymorphism (SNP) for accurate species differentiation and phylogenetic analysis confirmed different clusters for LCB. The study highlights the misidentification of L.petauri as L.garvieae in lactococcosis outbreaks and the importance of accurate species differentiation in disease management. The tuf gene sequencing method shows promise for practical, cost-effective, and accurate differentiation of closely related streptococcal species in aquaculture. These findings strongly indicate the need to re-evaluate the initial identification of isolates from fish with lactococcisis. The findings of this study also suggest that the tuf gene sequencing, established in this research for its practicality and cost-efficiency, could potentially be integrated into routine diagnostic procedures for Gram-positive, catalase-negative cocci associated with outbreaks of infections in aquatic animals; however, further experimental works are warranted.
•Lactococcus petauri is pathogenic to rainbow trout in Iran.•The analysis of the tuf gene sequence allowed for the correct identification of Gram-positive catalase-negative cocci•The analysis of the tuf gene sequence is capable of discrimination between L. garvieae and L. petauri.•This is the first report of L. petauri in Iran.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The study investigated the genetic diversity and population structure of Candidatus P. aurantifolia using tuf gene sequences sourced from GenBank™. A total of 29 sequences were analyzed based on ...location availability, unveiling 8 distinct haplotypes. Haplotype 5, encompassing sequences from Egypt, Australia, and Thailand, emerged as the most prevalent. Phylogenetic analysis revealed two different major clades with a significant genetic divergence within species. Notably, calculated haplotype diversity ranged from 0.0 to 0.5909, with India exhibiting the highest diversity. Moreover, haplotype diversity (Hd) was absent in several regions, including Egypt, Australia, and Burkina Faso. Furthermore, nucleotide diversity varied across regions, with Oman displaying the highest value (0.78182) and Thailand showing the lowest (0.09422). A high raggedness index value in the populations of Oman, and Thailand and a low value in India. Substantial genetic divergence in the populations between India-Egypt with limited gene flow was evident by high values of DeltaSt, GammaSt and Fst. Fu Fs values, indicative of demographic expansions or selection events, were notably high in India (34.035). Significant Tajima D values (2.035) in India further support deviations from neutral evolution. Our findings provide unprecedented insights into the population genetics and haplotype network of Candidatus P. aurantifolia, shedding light on its genetic diversity and geographic distribution in different countries. The study results will aid in the prediction of bacterium transmission and the implementation of effective quarantine measures. Moreover, the identification of regions having high genetic divergence and unique haplotypes may help in developing disease management strategies for targeted areas.
•Candidatus Phytoplasma aurantifolia is associated with numerous plant diseases.•tuf gene seems to be a potential candidate for understanding the population genetics of Candidatus P. aurantifolia.•Eight distinct haplotypes have been revealed in Candidatus P. aurantifolia.•The calculated haplotype diversity ranged from 0 to 0.5909, with India exhibiting the highest diversity.•Significant genetic divergence in Candidatus P. aurantifolia populations between India-Egypt with limited gene flow.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
In order to devise a method for rapid detection of ‘Candidatus (Ca.) Phytoplasma pini’ and for distinguishing it rapidly from other phytoplasmas, we carried out preliminary sequencing of Lithuanian ...‘Ca. Phytoplasma pini’ strain PineBL2 using Illumina (NGS) technology and targeted sequencing employing universal phytoplasma primers. We focused on two resulting chromosomal segments that contained a 16S rRNA gene and a translation elongation factor EF‐TU gene (tuf), respectively. Based on alignments of the ‘Ca. Phytoplasma pini’ gene sequences with the corresponding sequences of other phytoplasmas, we designed new primer pairs for PCR‐based detection of ‘Ca. Phytoplasma pini’. Because ‘Ca. Phytoplasma pini’ strains are expected to reside in the pine phloem in a very low titre, one might expect that they could be detected only by nested PCR. By contrast, the primers and PCR protocols designed in the current work enabled rapid direct PCR detection and identification of ‘Ca. Phytoplasma pini’ by amplifying a 484 bp 16S rDNA segment and a 513 bp tuf gene fragment that contain regions unique to this phytoplasma.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Arcanobacterium canis is a novel species of the Arcanobacterium most closely related to A. haemolyticum. This study aims to characterize two A. canis isolates recovered from companion animals, ...specifically the claw of a cat and a vaginal swab from a dog. This study used real-time PCR to characterize A. canis isolated from companion animals. Two isolates of A. canis were recovered from purulent material from the claw of an 11-year-old cat in Germany and a vaginal swab of a dog in the United Kingdom. The samples were characterized phenotypically and genotypically. Both isolates were analyzed using culture methods, biochemical analysis, MALDI-TOF MS, real-time PCR amplification and sequencing of the 16S rRNA gene, and rpoB, gap, and tuf genes. The findings showed that the isolates P5197-15 and M214-96-1 obtained from companion animals were successfully characterized and confirmed to species level by real-time PCR amplification and sequencing of the 16S rRNA gene, as well as the genes of rpoB, gap, and tuf. This study seeks to comprehensively understand the characteristics of A. canis isolates obtained from companion animals. Such knowledge is essential for accurate diagnosis, treatment, and control of infections caused by this pathogen in veterinary medicine. Additionally, it contributes to the broader understanding of the genetic diversity and characteristics of A. canis, which can have implications for public health and animal well-being.
Membrane with molecular selectivity, low fouling propensity and low pressure application is beneficial for effective separation. Designing a multipurpose tight ultrafiltration (M-TUF) membrane is ...challenging, yet requires for facile separation. Our design towards M-TUF membrane is based on the porous base substrate with rough morphology and weak electrostatic effect towards relatively smaller size ions and greater sieving and charge effect of selective layer towards relatively bigger sized molecules. Layer-by-layer (LbL) assembly of polyelectrolytes on a rough cationic poly(vinylidene fluoride) (PVDF-NMe3) substrate leads to the formation of TUF membranes. The molecular weight cutoff (MWCO) sharply reduces from about 4 × 105 g mol−1 (base substrate) to about 4 × 103 g mol−1 and 2 × 103 g mol−1 respectively after fourth and fifth layers of LbL assembly. The membranes (fifth and seventh layers) obtained under optimized conditions show low pressure-driven (0.68 bar) selective removal of Rose Bengal (RB, rejection∼99.5% and 99.9%) and Reactive black (RB-5, rejection∼96.8% and 99.2%) from feeds containing dye and monovalent (NaCl rejection<10%) or dye and divalent (MgCl2 rejection <30%) salts with steady permeate flux. Representative salt (MgCl2) to RB selectivity values for the two membranes are 164 and 720 respectively. Membranes obtained after third and fifth layers of LbL assembly show water permeance in the range of 71–105 Lm−2h−1bar−1 and flux recovery ratio of 81–85% for the separation of oil-in-water emulsions. The preparation process is extended using copolymer polyelectrolyte for the quick LbL assembly to obtain low fouling membrane. This work provides an insight to obtain TUF membrane for low pressure-driven molecular separation.
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•LbL assembly of polyelectrolytes was performed to obtain tight UF membranes.•Morphology of base substrate influenced the water wetting and antifouling property.•The membranes showed separation of dyes and salts with high selectivity.•The membranes showed steady performance during dye separation.•The membranes showed antifouling property during oil-in-water emulsion separation.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Grapevine (
L.) is one of the most important horticultural crops in Iran, with >200,000 ha of cultivated area. Recently, outbreaks of the grapevine yellows Bois noir that is associated with ...phytoplasma strains related to '
Phytoplasma solani' were recorded in several Iranian regions. This has resulted in severe economic losses. We carried out a survey in 2015, followed by collection of leaf samples from symptomatic grapevines and weeds. Because no information is available on the molecular epidemiology of '
P. solani' in Iran, multiple gene analyses were carried out here according to molecular characterization of the
and
1 genes. From the molecular characterization, all of the samples (i.e., grapevines, weeds) were infected with
b type. Detailed molecular characterization of the
1 gene (i.e., PCR-restriction fragment length polymorphism, sequence analysis) defined five molecular types: V1, V4, V10, V15, and V20. The abundance of
in vineyards and detection of the same '
. P. solani' molecular types in grapevines and weeds suggest that
has a major role in Bois noir epidemiology of Iranian vineyards. Therefore, control strategies should be developed to manage these host plants to reduce inoculum sources of the phytoplasma in vineyards.
Viability is a prerequisite for any therapeutic benefits associated with the ingestion of probiotic bacteria. Current culture-based techniques are inadequate for the enumeration of probiotics in ...mixed-species food products. This study utilized a quantitative PCR (qPCR) method coupled with propidium monoazide (PMAxx), and novel species-specific
gene primers to selectively enumerate
spp., and yogurt starter cultures in mixed-species probiotic yogurt. The method was optimized for PMAxx concentration and specificity and evaluated for efficiency and applicability. PMAxx-qPCR showed high specificity to the target organisms in mixed-species yogurt, quantifying only viable cells. The linear dynamic ranges were established over five to seven orders of magnitude. The assay was reliable with an efficiency of 91-99%,
values > 0.99, and a good correlation to the plate count method (
= 0.882). The results of this study demonstrate the high selectivity, improved lead time, and reliability of PMAxx-qPCR over the culture-dependent method, making it a valuable tool for inline viability verification during processing and improving probiotic quality assurance for processors and consumers.
MRSA is an increasing problem in humans as well as livestock. The bacterial co-colonization of the skin in MRSA carriers has been poorly investigated and moreover, there have been no methods for high ...resolution investigations of the Staphylococcus genus apart from tediously culturing or doing multiple PCRs. On 120 samples from pig ear, skin and nose, we generated amplicons from the V1-V2 region of the 16S rRNA gene to gather an overview of the genus-level microbiome, along with using MRSA specific plates to count MRSA. In parallel with this, amplicons of the tuf gene were generated, targeting only a region of the tuf gene found only in the Staphylococcus genus. Using these methods, we determined a core microbiota across the healthy pig and determined the Staphylococcus genus to be dominated by S. equorum. Moreover, we found Streptococcus to be inversely associated with Staphylococcus and MRSA, suggesting a role for this genus in combating MRSA. In this work, we have thoroughly investigated the skin and nose microbiome of the pig and developed a high throughput method for profiling the Staphylococcus genus which we believe will be useful for further investigations.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
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