Genomic analysis of Helicobacter pylori in Australia: Antimicrobial resistance, phylogenetic patterns, and virulence factors.

BACKGROUND AND AIM: Rates of antimicrobial-resistant Helicobacter pylori infection are rising globally, but little is known about contemporary resistance patterns, virulence factors, and phylogenetic patterns of isolates within Australia. We aimed to characterize antimicrobial resistance and genetic mutations associated with adverse clinical outcomes. METHODS: Whole genome sequencing, culturing, and antibiotic sensitivity data for refractory H. pylori isolates at Australian centers were collected between 2013 and 2022. Phylogenetic origins, antibiotic resistance mutations, and virulence factors were examined with phenotypic resistance profiles. RESULTS: One hundred thirty-five isolates underwent culture, with 109 of these undergoing whole genome sequencing. Forty-three isolates were isolated from patients in South Australia and 66 from Western Australia. Isolates originated primarily from hpEurope (59.6%), hpEastAsia (25.7%), and hpNEAfrica (6.4%). Antimicrobial resistance to clarithromycin was seen in 85% of isolates, metronidazole in 52%, levofloxacin in 18%, rifampicin in 14%, and amoxicillin in 9%. Most isolates (59%) were multi-drug resistant. Resistance concordance between genetically determined resistance and phenotypic resistance was 92% for clarithromycin and 94% for levofloxacin. Analysis of virulence factors demonstrated cag pathogenicity island (cagPAI) in 67% of isolates and cagA in 61%, correlating with isolate genetic origin. The most virulent s1m1 vacuolating cytotoxin A genotype was present in 26% of isolates. CONCLUSION: Refractory H. pylori isolates in Australia emanate from multiple global origins. Strong concordance between genetic and phenotypic antibiotic resistance profiles raises the possibility of utilizing genetic profiling in clinical practice. The dynamic landscape of H. pylori in Australia warrants the establishment of a national database to monitor H. pylori resistance and evolving virulence.

Efficacy and safety of acupuncture for depression: A systematic review and meta-analysis.

Acupuncture is widely accepted as a therapeutic option for managing depression. However, evidence from clinical trials remains controversial. This review aims to synthesize the best available evidence on the efficacy and safety of acupuncture in managing depression. The review was performed according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analysis) guidelines. Five databases and the relevant trial registries were searched from the inception to October 2021. Randomized clinical trials of acupuncture for managing depression, published in English, were selected for inclusion. The quality of included studies was assessed using the Cochrane risk of bias tool. Netmeta and dmetar of R packages were used to conduct a network meta-analysis. Twenty-two trials with 2391 participants were eligible and included in the analysis. This review found evidence that electroacupuncture (EA) plus antidepressant achieved superior outcomes compared with the waitlist (standardized mean difference = -8.86, 95% confidence interval: -14.78 to -2.93). The treatment ranking of different interventions in improving depression symptoms indicated that EA plus antidepressant with a probability of 0.8294, followed by manual acupuncture (MA) plus antidepressant (0.6470) and MA (0.5232). Acupuncture, either in isolation or as an adjunct to pharmacological treatment, has clinical benefits and can be considered a safe option for managing depression.

Dysfunctional Gut Microbiome Networks in Childhood IgE-Mediated Food Allergy.

The development of food allergy has been reported to be related with the changes in the gut microbiome, however the specific microbe associated with the pathogenesis of food allergy remains elusive. This study aimed to comprehensively characterize the gut microbiome and identify individual or group gut microbes relating to food-allergy using 16S rRNA gene sequencing with network analysis. Faecal samples were collected from children with IgE-mediated food allergies (n = 33) and without food allergy (n = 27). Gut microbiome was profiled by 16S rRNA gene sequencing. OTUs obtained from 16S rRNA gene sequencing were then used to construct a co-abundance network using Weighted Gene Co-expression Network Analysis (WGCNA) and mapped onto Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. We identified a co-abundance network module to be positively correlated with IgE-mediated food allergy and this module was characterized by a hub taxon, namely Ruminococcaceae UCG-002 (phylum Firmicutes). Functional pathway analysis of all the gut microbiome showed enrichment of methane metabolism and glycerolipid metabolism in the gut microbiome of food-allergic children and enrichment of ubiquinone and other terpenoid-quinone biosynthesis in the gut microbiome of non-food allergic children. We concluded that Ruminococcaceae UCG-002 may play determinant roles in gut microbial community structure and function leading to the development of IgE-mediated food allergy.

Children with nut allergies have impaired gene expression of Toll-like receptors pathway.

BACKGROUND: Trends in food allergies prompted investigation into the underlying mechanisms. Genetic and epigenetic factors are of high interest, and, in particular, the interplay between genes relating to immune factors directly and indirectly involved in food allergy pathogenesis. We sought to determine potential links between gene expression and epigenetic factors relating to Toll-like receptor (TLR) pathways and childhood food allergies. METHODS: In a cross-sectional study, samples from 80 children with and without food allergies were analysed for gene expression, DNA methylation and a range of immune factors relating to TLR pathways. TLR2, TLR4, CD14, IL5, IL13 and vitamin D were explored. RESULTS: The importance of these immune factors appeared to vary between the different types of food allergies. Expression of TLR2 (P < .001), TLR4 (P = .014) and CD14 (P = .028) varied significantly between children with no food allergy, allergy to nuts and peanuts, and allergy to eggs. DNA methylation in the promoter regions of these genes had a significant association with gene expression. These trends persisted when subjects were stratified by nut allergy vs no nut allergy. Furthermore, TLR2 (P = .001) and CD14 (P = .007) expressions were significantly lower in children with food allergies when compared to those without. CONCLUSION: Gene expression of TLR pathway genes was directly related to food allergy type, and DNA methylation had an indirect effect. TLR2 pathways are of significant interest in nut allergies.

The gut microbiota, environmental factors, and links to the development of food allergy.

Food allergy appears to have its roots in an insufficient exposure to a diverse range of environmental microbiota during early life. Microbial exposure ensures the colonization of the gastrointestinal tract with commensal microbes, which is necessary for the induction of a balanced and tolerogenic immune function. High-throughput sequencing technology has facilitated in-depth studies of the gut microbiota as well as bacterial-derived metabolites. Although the role of the microbiota in allergies is now widely studied, its importance for food allergy was only recently noted. Studies in human cohorts have shown that there is an association of dysbiosis and pathogenesis of food allergy, while studies from animal models have demonstrated the capacity of specific species in the gut microbiota to alter immune response, which may lead to the desensitization of food allergy. This article reviews the role of the gut microbiota in food allergy, and discusses the influence of environmental factors as well as prevention and management strategies relating to such regulatory mechanism.

The Implications of DNA Methylation on Food Allergy.

Food allergy is a major clinical and public health concern worldwide. The risk factors are well defined, however, the mechanisms by which they affect immune development remain largely unknown, and unfortunately the effective treatment or prevention of food allergy is still being researched. Recent studies show that the genes that are critical for the development of food allergy are regulated through DNA methylation. Environmental factors can affect host DNA methylation status and subsequently predispose people to food allergy. DNA methylation is therefore an important mediator of gene-environment interactions in food allergy and key to understanding the mechanisms underlying the allergic development. Indeed, the modification and identification of the methylation levels of specific genetic loci have gained increasing attention for therapeutic and diagnostic application in combating food allergy. In this review, we summarize and discuss the recent developments of DNA methylation in food allergy, including the pathogenesis, therapy, and diagnosis. This review will also summarize and discuss the environmental factors that affect DNA methylation levels in food allergy.

Nitrogen removal and water microbiota in grass carp culture following supplementation with Bacillus licheniformis BSK-4.

This experiment was designed to study the effects of Bacillus licheniformis BSK-4 on nitrogen removal and microbial community structure in a grass carp (Ctenopharyngodon idellus) culture. The selected strain Bacillus licheniformis BSK-4 significantly decreased nitrite, nitrate and total nitrogen levels in water over an extended, whereas increased ammonia level. Pyrosequencing showed that Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were dominant in grass carp culture water. Compared with the control group, the number of Proteobacteria and Firmicutes were increased, while Actinobacteria and Bacteroidetes decreased in treatment group. At the genus level, some genera, such as Bacillus, Prosthecobacter, Enterococcus, etc., appear only in the treatment, while many other genera exist only in the control group; Lactobacillus, Luteolibacter, Phenylobacterium, etc. were increased in treatment group compared to those in control group. As above, the results suggested that supplementation with B. licheniformis BSK-4 could remove some nitrogen and cause alterations of the microbial composition in grass carp water.

Participants experiences regarding the use of acupuncture as a treatment modality: A qualitative systematic review.

BACKGROUND: Acupuncture is a promising modality in clinical practice, where the participants' experiences are crucial to acupuncture's use and effects. However, a comprehensive review synthesising participant experiences throughout treatment sessions is lacking. This study aims to explore the qualitative literature regarding participants' experiences of acupuncture as a potential treatment modality. METHODS: A qualitative systematic review of existing literature was conducted through AMED, MEDLINE, Scopus, Embase, and Web of Science. The Joanna Briggs Institute (JBI) critical appraisal checklist was employed to evaluate research quality. Subsequently, the data were extracted and synthesised utilising the JBI Qualitative Assessment and Review Instrument (QARI) tool and data synthesis was carried out through meta-aggregation. RESULTS: A total of twenty-eight articles were incorporated into the analysis. Four synthesised findings were identified: (1) Before acupuncture: last trust and hope; (2) During acupuncture: relaxing and calming; (3) After acupuncture: mind-body effects; and (4) Practitioner-participant relationship. CONCLUSION: The findings highlight the changes participants experienced before and after acupuncture sessions. Implementing additional promotional initiatives for acupuncture can increase public awareness and encourage individuals to consider it an early symptom management option. REVIEW REGISTRATION: This review was registered in PROSPERO (No. CRD42023475373).

Association Between Biofilm Formation and Structure and Antibiotic Resistance in H. pylori.

Background: Persistent infections caused by Helicobacter pylori (H. pylori), which are resistant to antibiotic treatment, pose a growing global public health concern. Biofilm formation is known to be associated with persistent infections due to its role in enhancing antimicrobial resistance and the tolerance of many pathogenic bacteria. Objective: This study aims to evaluate the biofilm formation of clinical isolates of H. pylori and its impact on antibiotic eradication. Methods: The thickness, morphology, and structure of biofilms derived from nine H. pylori strains were examined using confocal laser scanning microscopy, scanning electron microscopy, and transmission electron microscopy. Subsequently, the susceptibility of both planktonic and biofilm bacteria was assessed through the determination of minimum inhibitory concentration and minimum biofilm eradication concentration for amoxicillin, clarithromycin, levofloxacin, and tetracycline. Results: The results revealed varying biofilm thicknesses and densities among the strains, characterised by the presence of numerous filaments intertwining and connecting bacterial cells. Additionally, several cases exhibited susceptibility based on MIC measurements but resistance according to MBEC measurements, with MBEC indicating a higher resistance rate. Pearson Correlation analysis demonstrated a positive correlation between biofilm thickness and MBEC results (0 < r < 1), notably significant for amoxicillin (r = 0.801, P = 0.009) and tetracycline (r = 0.696, P = 0.037). Conclusion: Different strains of H. pylori exhibit variations in their capacity to release outer membrane vesicles (OMVs) and form biofilms. Biofilm formation can influence the effectiveness of amoxicillin and tetracycline in eradicating susceptible bacterial strains.

Efficacy and Safety of Acupuncture and or Moxibustion for Managing Primary Dysmenorrhea: A Systematic Review and Meta-Analysis.

Acupuncture and moxibustion have been accepted as add-on options for primary dysmenorrhea (PD); however, the clinical evidence is still inadequate. We searched AMED, CENTRAL, EMBASE, PubMed, Web of Science, CBM, CNKI, VIP, Wangfang database, ANZCTR, ClinicalTrials.gov, and the WHO ICTRP, from their inception to February 2021. The pooled analysis of 13 RCTs with 675 participants for VAS showed that acupuncture and moxibustion were more effective in managing PD than the control group with the MD of -1.93 (95% CI [-2.80, -1.06] and -2.67 (95% CI [-4.96, -0.38]). With the CMSS, seven studies with 487 participants showed that these modalities were more effective than the control group with the MD of -7.58 (95% CI [-10.97, -4.19]) and -3.78 (95% CI [-6.90, -0.66]). The findings indicated that acupuncture and moxibustion could relieve pain effectively and has fewer adverse events (AEs) in managing PD.

Research methodology in acupuncture and moxibustion for managing primary dysmenorrhea: A scoping review.

BACKGROUND: Acupuncture and moxibustion have promising effects in managing primary dysmenorrhea. However, some evidence from clinical trials remains controversial due to methodological flaws in study designs that involve acupuncture and its related modalities and require urgent attention and dialogue. METHODS: Allied and Complementary Medicine Database (AMED), Cochrane Library, Excerpta Medica database (EMBASE), PubMed, Web of Sciences, Chinese Biological Medicine (CBM), China National Knowledge Infrastructure (CNKI), VIP Database for Chinese Technical Periodicals (VIP), and Wanfang database were searched from their inception to July 2021. Data were extracted based on the types of study design, primary outcome measures, adverse events (AEs), and participants' subjective views. RESULTS: Most studies (n = 282, 93 %) were published in Chinese and 21 (7 %) in English. Among these, there were 209 (69 %) randomized controlled trials (RCTs), 39 (13 %) non-randomized controlled trials (nRCTs), 30 (10 %) case-series reports, 15 (5 %) cohort studies, and 10 (3 %) case reports. The most frequent reported outcome was pain, followed by emotion, sleeping quality, quality of life, skin temperature, changes in brain function, uterine and ovarian blood flow, and reproductive endocrine level. AEs were reported in 37 studies with mild events, and all recovered without actions taken; 31 trials reported no AEs; 235 failed to report any AEs. One RCT found that the satisfaction rate of the intervention group was statistically significantly higher than the control group. CONCLUSION: Clinical studies on acupuncture and its related modalities face methodological challenges and require urgent attention. RCT with blinding and sham control might be the gold standard trial design. However, it may not be the most suitable research method for these modalities. We recommend using pragmatic RCTs in this field, where trial protocol registration on the trial registry platforms and detailed safety reporting should be mandatory.

Identifying gene network patterns and associated cellular immune responses in children with or without nut allergy.

BACKGROUND: Although evidence suggests that the immune system plays a key role in the pathophysiology of nut allergy, the precise immunological mechanisms of nut allergy have not been systematically investigated. The aim of the present study was to identify gene network patterns and associated cellular immune responses in children with or without nut allergy. METHODS: Transcriptome profiling of whole blood cells was compared between children with and without nut allergy. Three genes were selected to be validated on a larger cohort of samples (n = 86) by reverse transcription-polymerase chain reactions (RT-qPCR). The composition of immune cells was inferred from the transcriptomic data using the CIBERSORTx algorithm. A co-expression network was constructed employing weighted gene co-expression network analysis (WGCNA) on the top 5000 most variable transcripts. The modules were interrogated with pathway analysis tools (InnateDB) and correlated with clinical phenotypes and cellular immune responses. RESULTS: Proportions of neutrophils were positively correlated and CD4+ T-cells and regulatory T-cells (Tregs) were negatively correlated with modules of nut allergy. We also identified 2 upregulated genes, namely Interferon Induced With Helicase C Domain 1 (IFIH1), DNA damage-regulated autophagy modulator 1 (DRAM1) and a downregulated gene Zinc Finger Protein 512B (ZNF512B) as hub genes for nut allergy. Further pathway analysis showed enrichment of type 1 interferon signalling in nut allergy. CONCLUSIONS: Our findings suggest that upregulation of type 1 interferon signalling and neutrophil responses and downregulation of CD4+ T-cells and Tregs are features of the pathogenesis of nut allergy.