Mutational and Transcriptomic Changes Involved in the Development of Macrolide Resistance in Campylobacter jejuni

Macrolide antibiotics are important for clinical treatment of infections caused by Campylobacter jejuni. Development of resistance to this class of antibiotics in Campylobacter is a complex process, and the dynamic molecular changes involved in this process remain poorly defined. Multiple lineages of macrolide-resistant mutants were selected by stepwise exposure of C. jejuni to escalating doses of erythromycin or tylosin. Mutations in target genes were determined by DNA sequencing, and the dynamic changes in the expression of antibiotic efflux transporters and the transcriptome of C. jejuni were examined by real-time reverse transcription-PCR, immunoblotting, and DNA microarray analysis. Multiple types of mutations in ribosomal proteins L4 and L22 occurred early during stepwise selection. On the contrary, the mutations in the 23S rRNA gene, mediating high resistance to macrolides, were observed only in the late-stage mutants. Upregulation of antibiotic efflux genes was observed in the intermediately resistant mutants, and the magnitude of upregulation declined with the occurrence of mutations in the 23S rRNA gene. DNA microarray analysis revealed the differential expression of 265 genes, most of which occurred in the intermediate mutant, including the upregulation of genes encoding ribosomal proteins and the downregulation of genes involved in energy metabolism and motility. These results indicate (i) that mutations in L4 and L22 along with temporal overexpression of antibiotic efflux genes precede and may facilitate the development of high-level macrolide resistance and (ii) that the development of macrolide resistance affects the pathways important for physiology and metabolism in C. jejuni, providing an explanation for the reduced fitness of macrolide-resistant Campylobacter

Genome plasticity of Vibrio parahaemolyticus: microevolution of the 'pandemic group'

<p>Abstract</p> <p>Background</p> <p>Outbreak of <it>V. parahaemolyticus </it>infections occurred since 1996 was linked to a proposed clonal complex, the pandemic group. The whole genome sequence provides an unprecedented opportunity for dissecting genome plasticity and phylogeny of the populations of <it>V. parahaemolyticus</it>. In the present work, a whole-genome cDNA microarray was constructed to compare the genomic contents of a collection of 174 strains of <it>V. parahaemolyticus</it>.</p> <p>Results</p> <p>Genes that present variably in the genome accounted for about 22% of the whole gene pool on the genome. The phylogenetic analysis of microarray data generated a minimum spanning tree that depicted the phylogenetic structure of the 174 strains. Strains were assigned into five complexes (C1 to C5), and those in each complex were related genetically and phylogenetically. C3 and C4 represented highly virulent clinical clones. C2 and C3 constituted two different clonal complexes 'old-O3:K6 clone' and 'pandemic clone', respectively. C3 included all the 39 pandemic strains tested (<it>trh</it>^-, <it>tdh</it>⁺and GS-PCR⁺), while C2 contained 12 pre-1996 'old' O3:K6 strains (<it>trh</it>⁺, <it>tdh</it>^-and GS-PCR^-) tested herein. The pandemic clone (post-1996 'new' O3:K6 and its derivates O4:K68, O1:K25, O1:KUT and O6:K18) might be emerged from the old-O3:K6 clone, which was promoted by acquisition of <it>toxRS</it>/new sequence and genomic islands. A phylogenetic intermediate O3:K6 clade (<it>trh</it>^-, <it>tdh</it>^-and GS-PCR⁺) was identified between the pandemic and old-O3:K6 clones.</p> <p>Conclusion</p> <p>A comprehensive overview of genomic contents in a large collection of global isolates from the microarray-based comparative genomic hybridization data enabled us to construct a phylogenetic structure of <it>V. parahaemolyticus </it>and an evolutionary history of the pandemic group (clone) of this pathogen.</p

(2R,3S)-2-Benzyl-3-(2,3,4,6-tetra-O-acetyl-β-d-glucopyranos­yloxy)butanolide

The title compound, C25H30O12, which demonstrates a significant hepatoprotective effect, has comparable geometrical parameters to those of similar compounds. The absolute configuration of the title compound, viz. 2R,3S, was identified from the Flack parameter of 0.05 (17) and the Hooft parameter of 0.04 (6)

Three-dimensional petrographical investigations on borehole rock samples: a comparison between X-ray computed- and neutron tomography

Technical difficulties associated with excavation works in tectonized geological settings are frequent. They comprise instantaneous and/or delayed convergence, sudden collapse of gallery roof and/or walls, outpouring of fault-filling materials and water inflows. These phenomena have a negative impact on construction sites and their safety. In order to optimize project success, preliminary studies on the reliability of rock material found on site are needed. This implies in situ investigations (surface mapping, prospective drilling, waterflow survey, etc.) as well as laboratory investigations on rock samples (permeability determination, moisture and water content, mineralogy, petrography, geochemistry, mechanical deformation tests, etc.). A set of multiple parameters are then recorded which permit better insight on site conditions and probable behavior during excavation. Because rock formations are by nature heterogeneous, many uncertainties remain when extrapolating large-scale behavior of the rock mass from analyses of samples order of magnitudes smaller. Indirect large-scale field investigations (e.g. geophysical prospecting) could help to better constrain the relationships between lithologies at depth. At a much smaller scale, indirect analytical methods are becoming more widely used for material investigations. We discuss in this paper X-ray computed tomography (XRCT) and neutron tomography (NT), showing promising results for 3D petrographical investigations of the internal structure of opaque materials. Both techniques record contrasts inside a sample, which can be interpreted and quantified in terms of heterogeneity. This approach has the advantage of combining genetic parameters (physico-chemical rock composition) with geometric parameters resulting from alteration or deformation processes (texture and structure). A critical analysis of such 3D analyses together with the results of mechanical tests could improve predictions of short- and long-term behavior of a rock unit. Indirect methods have the advantage of being non-destructive. However, as it is the case with large-scale geophysical surveying, XRCT and NT are affected by several error factors inherent to the interaction of a radiation modality (X-ray or neutron beam) with the atomic structure of the investigated materials. Recorded signals are therefore in particular cases not artifact-free and need to be corrected in a subsequent stage of data processin

Epidemiological characteristics analysis of foodborne disease outbreaks caused by takeaway in China’s Mainland from 2010 to 2020

ObjectiveTo analyze the epidemiological characteristics of foodborne disease outbreaks caused by takeaway in China’s Mainland from 2010 to 2020， and put forward relevant regulatory suggestions.MethodsThrough the National Foodborne Disease Outbreak Monitoring System， the data of foodborne disease outbreaks caused by takeaway in China’s Mainland from 2010 to 2020 were collected and analyzed， and descriptive epidemiological characteristics were performed.ResultsA total of 549 foodborne disease outbreaks caused by takeaway were reported in China’s Mainland （except Tibet Autonomous Region） from 2010 to 2020， resulting in 9 285 illnesses and 2 deaths. The largest number of outbreaks and illnesses was in the third quarter， accounting for 41.53% and 44.58% of the total respectively. Except the unknown pathogenic factors， the number of outbreaks and illnesses caused by microbial pathogenic factors were the highest， accounting for 39.16% and 60.26% of the total respectively. Except the unknown suspected food， the number of outbreaks and illnesses caused by mixed food and multiple food were higher， accounting for 21.86% and 15.12% of the outbreaks respectively， and accounting for 20.58% and 13.10% of the number of illnesses respectively. Except the unknown food source， the top 3 food source were school canteens， collective dining delivery units/central kitchens and fast food restaurants， the number of outbreaks accounted for 20.04%， 15.66% and 15.48% respectively， and the number of illnesses accounted for 35.30%， 17.52% and 10.57% respectively. Except the multiple factors and unknown factors， the number of outbreaks caused by improper storage were the highest accounting for 8.74%， and the number of illnesses caused by improper processing accounted for 7.74%.ConclusionMicrobial growth and reproduction due to improper storage and processing is the major cause of foodborne disease outbreaks caused by takeaway. It is suggested that the food safety supervision and administration departments should strengthen the whole process supervision and management of takeaway， establish and ensure catering services strictly abide by the good hygiene operations according to food raw in materials， production， transportation， distribution and other aspects， so as to effectively prevent and control the occurrence foodborne diseases

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family