Characteristics of Helicobacter pylori Heteroresistance in Gastric Biopsies and Its Clinical Relevance.

BACKGROUND: Antimicrobial susceptibility testing (AST) plays a vital role in anti-Helicobacter pylori treatment, but the traditional AST method has difficulty detecting heteroresistance, which may cause an increased prevalence of resistant strains and eradication failure. AIMS: To investigate the characteristics of heteroresistance in H. pylori in gastric biopsies and investigate its clinical relevance. METHOD: A total of 704 gastric biopsies were selected for 23S rRNA and gyrA gene sequencing, 470 H. pylori isolates from these biopsies were selected for AST, and the clinical characteristics of the patients were reviewed. RESULT: For the 699 biopsies that were positive for 23S rRNA gene, 98 (14.0%) showed a heteroresistance genotype, and a wild type (WT) combined with A2143G (86.7%) genotype was found in most samples. For the 694 biopsies that were positive for gyrA gene, 99 (14.3%) showed a heteroresistance genotype, and a WT combined with 87K (26.3%) or WT combined with 91N (23.2%) genotype was predominant. According to the E-test results, the resistance rates of heteroresistance genotype samples for clarithromycin and levofloxacin were 36.2% and 68.1%, respectively. When dividing the heteroresistance samples into different groups according to the sequencing profile peaks of the mutation position, the resistance rates were higher along with mutation peaks at the mutation position. In addition, patients infected with mutated or heteroresistant strains showed lower peptic ulcer detection rates than those infected with the WT strain (p < 0.05). CONCLUSION: Heteroresistance genotypes for clarithromycin and levofloxacin were not rare in H. pylori. Most cases with a heteroresistance genotype showed a susceptible phenotype for clarithromycin and a resistance phenotype for levofloxacin. Patients infected with heteroresistance genotype strains showed a lower peptic ulcer detection rate than those infected with the WT strain.

Genotype profiles of Helicobacter pylori from gastric biopsies and strains with antimicrobial-induced resistance.

BACKGROUND AND AIMS: The genotypic method could significantly shorten the time needed to obtain antibiotic susceptibility data for Helicobacter pylori. The aim of this study was to explore the profile of H. pylori from gastric biopsies and strains with antibiotic-induced resistance. METHODS: A total of 124 gastric biopsies were used to perform gene sequencing and to perform bacterial culture and susceptibility testing. Seven susceptible strains were selected to develop resistance to clarithromycin, levofloxacin, and metronidazole. Four susceptible strains were selected to transfer candidate mutations. The genotype profiles of these groups were analyzed by sequencing analysis. The antibiotic susceptibility of these strains was detected using the E-test method. RESULTS: Phenotypic resistance to clarithromycin, levofloxacin, and metronidazole was observed in 35.5%, 40.0%, and 79.8% strains, respectively. Point mutations in 23 S rRNA, gyrA, and rdxA genes were observed in 39.5%, 38.7%, and 86.3% of gastric biopsies, respectively. The A2143G mutation in the 23S rRNA occurs in most clarithromycin-resistant samples. The A2142C point mutation showed a higher efficacy than A2142G and A2143G for inducing clarithromycin resistance. The D91N and N87K mutations in gyrA occurs in most levofloxacin-resistant samples, and double point mutations showed a higher efficacy than single mutations for inducing levofloxacin resistance. Phenotypic resistance and mutations in rdxA lacked consistency. CONCLUSION: Genotype-based gastric biopsy analysis was reliable for determining clarithromycin and levofloxacin resistance. A2143G in 23S rRNA and N87K/D91N in the gyrA gene occurred in most resistant strains. Mutations in the rdxA gene were not good indicators of metronidazole resistance.

[The impact of phylogenetic uncertainty on the metrics of community phylogenetic structure]. / ç‰©ç§è°±ç³»ä¸ç¡®å®šæ€§å¯¹ç¾¤è½è°±ç³»æ ¼å±€æŒ‡æ ‡çš„å½±å“.

Phylogeny has been widely used to quantify community phylogenetic structure and to infer the underlying mechanism. Many studies, however, neglected phylogeny uncertainty and its potential impact on community phylogenetic structure. In this study, we explored the potential impact of phylogenetic uncertainty among 150 species in a 20 hm2 plot in Tiantong, Zhejiang. One consensus tree and 999 phylogenetic trees representing the phylogenetic uncertainty were estimated based on two cpDNA fragments (rbcL and matK). Combined with the species distribution data, community phylogenetic structure was quantified by two common indices (NRI and NTI) and their significances were tested by the independent swap null model. Our results showed that tree topology and node age showed a large uncertainty. The uncertainty was larger for young species and significantly increased with mean phylogenetic distance. Phylogenetic uncertainty increased the variation of both standardized NRI and NTI in each quadrat. These impacts were independent between both indices in either spatial pattern or the degree of impact. NRI was more sensitive than NTI to the uncertainty. At community scale, phylogenetic uncertainty also affected the variation of the mean standardized NRI and NTI of all quadrats, with mean standard deviation of 0.37 and 0.077, respectively. Such a result suggests that mean standardized NRI at community level was more vulnerable to the phylogenetic uncertainty, which is consistent with the result at the sample level. Our findings showed that phylogenetic uncertainty could add different variation into the NRI and NTI series indices and might increase biases in the quantification of community phylogenetic structure and its underlying ecological processes. Our results implied that non-random community phylogenetic structure was probably overestimated in the previous studies which ignored phylogenetic uncertainty.

microRNA regulation of skin pigmentation in fish.

MicroRNAs (miRNAs) are endogenous small non-coding RNAs that play crucial roles in numerous biological processes. However, the role of miRNAs in skin color determination in fish has not been completely determined. Here, we identified that 13 miRNAs are differentially expressed between red and white skin. The analysis of miRNA spatial and temporal expression patterns suggests that miR-429 is a potential regulator of skin pigmentation. miR-429 silencing results in an obvious change in skin pigmentation. Bioinformatics analysis and a luciferase reporter assay show that miR-429 directly regulates expression of Foxd3 by targeting its 3'-untranslated (3'-UTR) region. miR-429 silencing leads to a substantial increase in the expression of Foxd3 in vivo, thereby repressing the transcription of MITF and its downstream genes, such as TYR, TYRP1 or TYRP2. These findings would provide a novel insight into the determination of skin color in fish.

Complete mitochondrial DNA sequence of the endangered Tarim schizothoracin (Schizothorax biddulphi Günther).

Tarim schizothoracin (Schizothorax biddulphi Günther) is an extremely endangered freshwater fish that thrives only in the Tarim River drainage in China. In this paper, we initially determined the complete mitochondrial genome of schizothoracin fishes. The mitochondrial genome of S. biddulphi was 16,585 bp long, which is similar to most vertebrates. It contains the same gene order and a similar number of gene or region including 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 putative control region.

Isolation and characterization of polymorphic microsatellite markers from Australia short-finned eel (Anguilla australis Richardson).

Seventeen microsatellite DNA loci from the Australian short-finned eel (Anguilla australis Richardson) were isolated and their amplification characteristics were described. The polymerase chain reaction primers were tested on 40 eel individuals. The primers amplified loci with relatively high numbers of alleles, ranging from five to 14 with an average of nine per locus. Mean observed heterozygosity (H(O) ) and expected heterozygosity (H(E) ) were 0.6779 and 0.7374, respectively, indicating that these markers would be useful for population studies. No loci deviated significantly from Hardy-Weinberg equilibrium (P = 0.05) and no evidence was found for genotypic disequilibrium among loci at a 5% significance level.