phenotypic and genetic characterization
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2021 ◽  
Vol 12 ◽  
Author(s):  
Eliana De Luca ◽  
Sonsiray Álvarez-Narváez ◽  
Grazieli Maboni ◽  
Rodrigo P. Baptista ◽  
Nicole M. Nemeth ◽  
...  

The Pasteurellaceae family has been associated with fatal diseases in numerous avian species. Several new taxa within this family, including Bisgaard taxon 40, have been recently described in wild birds, but their genomic characteristics and pathogenicity are not well understood. We isolated Bisgaard taxon 40 from four species of seabirds, including one sampled during a mass, multi-species mortality event in Florida, United States. Here, we present a comprehensive phenotypic and genetic characterization of Bisgaard taxon 40 and comparative genomic analysis with reference strains from the Pasteurellaceae family, aiming at determining its phylogenetic position, antimicrobial susceptibility profile, and identifying putative virulence factors. In silico multilocus sequence-based and whole-genome-based phylogenetic analysis clustered all Bisgaard taxon 40 strains together on a distinct branch separated from the other members of the Pasteurellaceae family, indicating that Bisgaard taxon 40 could represent a new genus. These findings were further supported by protein similarity analyses using the concatenation of 31 conserved proteins and other taxonomic approaches such as the percentage of conserved protein test. Additionally, several putative virulence factors were identified, including those associated with adhesion (capsule, ompA, ompH) and colonization (exbD, fur, galU, galE, lpxA, lpxC, and kdsA) of the host and a cytolethal distending toxin (cdt), which may have played a role in disease development leading to the mortality event. Considerably low minimum inhibitory concentrations (MICs) were found for all the drugs tested, in concordance with the absence of antimicrobial resistance genes in these genomes. The novel findings of this study highlight genomic and phenotypic characteristics of this bacterium, providing insights into genome evolution and pathogenicity. We propose a reclassification of these organisms within the Pasteurellaceae family, designated as Mergibacter gen. nov., with Mergibacter septicus sp. nov. as the type species. The type strain is Mergibacter septicus A25201T (=DSM 112696).


Author(s):  
Shaowu Li ◽  
Jingru Chai ◽  
Christopher Knupp ◽  
Pierre Nicolas ◽  
Di Wang ◽  
...  

Flavobacterium psychrophilum causes substantial economic losses in salmonid aquaculture worldwide. Although this bacterium is also believed to be a disease source in China, published reports of its presence do not yet exist.


2021 ◽  
Vol 8 (4) ◽  
Author(s):  
Said Boudeffeur ◽  
Abdelkhader Ameur Ameur ◽  
M M Aci ◽  
Hafida Khelafi ◽  
Abdelkader Laaboudi ◽  
...  

Taqerbucht cultivars of date palm are well known by their natural resistance against devastating fungus Bayoud disease. In order to know, if these accessions have the same genetic and morphological profile or each of them constitutes a separate cultivar, we carried out a morphological and molecular characterization and we compared four Taqerbucht (Tq.) date palm cultivars from the southwestern region of Algeria: Tq.hamra cultivar (red fruits), Tq. safra cultivar (yellow fruits), Tq.beïda (white fruits) and Tq.kahla cultivar (black fruits). Seventy one phenotypic characteristics, including 33 quantitative and 38 qualitative traits, have been selected for comparison. Principal component analysis (PCA) and multi-component clustering were used to analyze and compare the data. The results suggest that the four cultivars can be classified into distinct groups. One group contains one cultivar, the Tq.kahla and another group contains the three other cultivars (Tq.safra, Tq.beïda and Tq. hamra). Based on phylogenetic analyses and sequence comparisons, the cultivar Tq. kahla seems to be divergent from the cultivar Tq.hamra, whereas the two cultivars Tq.Safra and Tq.beïda are close to each other. Using 16 Simple Sequence Repeat (SSR) genetic markers to analyze genetic diversity among the cultivars, we found that 13 markers were detectable in 31 allele's loci, and the number of alleles per locus varied from 1–4 with an average of 2.38 alleles per locus. Expected heterozygosity (He) values ranged from 0.375–0.500 and observed heterozygosity (Ho) values from 0.750–1.000.


2021 ◽  
Vol 12 ◽  
Author(s):  
Rob Van Houdt ◽  
Joachim Vandecraen ◽  
Wietse Heylen ◽  
Natalie Leys ◽  
Pieter Monsieurs ◽  
...  

Cupriavidus metallidurans strains display a decreased viability when incubated in rich medium at a temperature of 37°C compared to their normal growth temperature of 30°C, a phenomenon coined “temperature-induced mortality and mutagenesis” (TIMM). To scrutinize this aberrant phenotype further, the contributions of specific inducers and protective agents were determined. Different growth media, including lysogeny broth (LB) and Schatz, and components, including casamino acids, in particular amino acids (proline, cysteine, glycine, glutamine, leucine, histidine and phenylalanine) and ammonium, were found to induce TIMM at 37°C. Sorbitol was found to counteract TIMM. Furthermore, although TIMM is well conserved within the C. metallidurans species, multiple and strain-specific TIMM inducers exist. Twenty-nine percent of the TIMM survivors inherited resistance to TIMM. Whole-genome sequencing of two resistant derivatives revealed an important role of an uncharacterized oxidoreductase, indicating putative metabolic poisoning when grown in high-concentration nitrogen-containing media at 37°C.


2020 ◽  
Vol 11 ◽  
Author(s):  
Ye Wang ◽  
Liangying Zhong ◽  
Yan Xu ◽  
Lei Ding ◽  
Yuanjun Ji ◽  
...  

Multiple osteochondromas (MO), the most common type of benign bone tumor, is an autosomal dominant skeletal disorder characterized by multiple cartilage-capped bony protuberances. In most cases, EXT1 and EXT2, which encode glycosyltransferases involved in the biosynthesis of heparan sulfate, are the genes responsible. Here we describe the clinical, phenotypic and genetic characterization of MO in 22 unrelated Chinese families involving a total of 60 patients. Variant detection was performed by means of a battery of different techniques including Sanger sequencing and whole-exome sequencing (WES). The pathogenicity of the missense and splicing variants was explored by means of in silico prediction algorithms. Sixteen unique pathogenic variants, including 10 in the EXT1 gene and 6 in the EXT2 gene, were identified in 18 (82%) of the 22 families. Fourteen (88%) of the 16 variants were predicted to give rise to truncated proteins whereas the remaining two were missense. Seven variants were newly described here, further expanding the spectrum of MO-causing variants in the EXT1 and EXT2 genes. More importantly, the identification of causative variants allowed us to provide genetic counseling to 8 MO patients in terms either of preimplantation genetic testing (PGT) or prenatal diagnosis, thereby preventing the reoccurrence of MO in the corresponding families. This study is the first to report the successful implementation of PGT in MO families and describes the largest number of subjects undergoing prenatal diagnosis to date.


Author(s):  
Kaknokrat Chonsin ◽  
Neunghatai Supha ◽  
Chie Nakajima ◽  
Yasuhiko Suzuki ◽  
Orasa Suthienkul

Abstract Vibrio parahaemolyticus (VP) is a major cause of gastroenteritis outbreaks in Thailand and other countries due to the consumption of contaminated and undercooked seafood. However, there have been few reports of the molecular epidemiology of VP isolates from asymptomatic seafood handlers. Here, we report the phenotypic and genetic characterization of 61 VP isolates obtained from asymptomatic workers in two seafood processing plants. We found 24 O:K serotypes of which O11:KUT, O1:KUT and O3:KUT were the dominant serotypes. Analysis by PCR showed 12 isolates harbored either tdh or trh genes with the potential to be pathogenic VP strains. The presence of T3SS2α and T3SS2β genes was correlated with the presence of tdh and trh, respectively. Four tdh+ isolates were positive for pandemic marker. In this study, VP isolates were commonly resistant to ampicillin, cephazolin, fosfomycin and novobiocin. Phylogenetic analysis of VP1680 loci in 35 isolates from 17 asymptomatic workers, six gastroenteritis patients, seven environmental samples and five genomes from a database showed 22 different alleles. Gene VP1680 was conserved in tdh+ isolates and pandemic strains, that of trh + isolates was diverse. Asymptomatic workers carrying VP were the most likely source of contamination, which raises concerns over food safety in seafood processing plants.


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