Barry Marshall

Changes in the Gut Microbiome and Predicted Functional Metabolic Effects in an Australian Parkinson's Disease Cohort

Publisher: Frontiers Media SA

Date: 29-10-2021

DOI: 10.3389/FNINS.2021.756951

Abstract: Background: There has been increasing recognition of the importance of the gut microbiome in Parkinson’s disease (PD), but the influence of geographic location has received little attention. The present study characterized the gut microbiota and associated changes in host metabolic pathways in an Australian cohort of people with PD (PwP). Methods: The study involved recruitment and assessment of 87 PwP from multiple Movement Disorders Clinics in Australia and 47 healthy controls. Illumina sequencing of the V3 and V4 regions of the 16S rRNA gene was used to distinguish inter-cohort differences in gut microbiota KEGG analysis was subsequently performed to predict functional changes in host metabolic pathways. Results: The current findings identified significant differences in relative abundance and ersity of microbial operational taxonomic units (OTUs), and specific bacterial taxa between PwP and control groups. Alpha ersity was significantly reduced in PwP when compared to controls. Differences were found in two phyla (Synergistetes and Proteobacteria both increased in PwP), and five genera (C olidextribacter, Intestinibacter, Kineothrix, Agathobaculum , and Roseburia all decreased in PwP). Within the PD cohort, there was no association identified between microbial composition and gender, constipation or use of gastrointestinal medication. Furthermore, KEGG analysis identified 15 upregulated and 11 downregulated metabolic pathways which were predicted to be significantly altered in PwP. Conclusion: This study provides the first comprehensive characterization of the gut microbiome and predicted functional metabolic effects in a southern hemisphere PD population, further exploring the possible mechanisms whereby the gut microbiota may exert their influence on this disease, and providing evidence for the incorporation of such data in future in idualized therapeutic strategies.

Towards circular fashion – transforming pulp mills into hubs for textile recycling

Publisher: Royal Society of Chemistry (RSC)

Date: 2021

DOI: 10.1039/D1RA00168J

Abstract: Textile recycling can be integrated in pulp mills through the use of green liquor in the pretreatment of the textiles.

Helicobacteriology update

Publisher: CSIRO Publishing

Date: 21-05-2021

DOI: 10.1071/MA21025

Abstract: Helicobacter pylori colonises the gastric mucosa and is associated with various gastric diseases, including stomach cancer. At least 1 million new cases of stomach cancer cases are reported annually, and it is the fifth top cancer-killer in the world. Although H. pylori can be eradicated by a combination of antibiotics, the treatment success rate is declining due to the rise of antibiotic resistance. The same antibiotic combination must not be prescribed repeatedly. Susceptibility guided precision medicine is the most effective strategy to combat antibiotic resistant H. pylori cases. In addition, maintaining a stomach pH ≥6 during the antibiotic treatment is an important factor to increase cure rates. The new type of acid blocker, P-CABs, have shown promising results in H. pylori treatment. Natural products may suppress the H. pylori growth or relieve the symptoms but have not been successful in solving the root of the problem. New combination therapies show promise and the dream of 100% cure of the infection with minimal side effects from treatment seems achievable. The next decade will see combination therapies with newer acid blockers in widespread use at reasonable cost.

Helicobacter pyloriinfection as a protective factor against multiple sclerosis risk in females

Publisher: BMJ

Date: 19-01-2015

DOI: 10.1136/JNNP-2014-309495

Abstract: In recent years, a relationship between Helicobacter pylori and many disease conditions has been reported, however, studies in its relationship with multiple sclerosis (MS) have had contradictory results. To determine the association between the H. pylori infection and MS. 550 patients with MS were included in the study and were matched by gender and year of birth to 299 controls. Patients were assessed for clinical and demographic parameters. An enzyme immunoassay was used to detect the presence of specific IgG antibodies against H. pylori in the serum s le of both groups. H. pylori seropositivity was found to be lower in the patients with MS than in controls (16% vs 21%) with the decrease pertaining to females (14% vs 22%, p=0.027) but not males (19% vs 20%, p=1.0). When adjusted for age at onset, year of birth and disease duration, H. pylori seropositive females presented with a lower disability score than seronegative females (p=0.049), while among males the reverse was true (p=0.025). There was no significant association between H. pylori seropositivity and relapse rate. Our results could reflect a protective role of H. pylori in the disease development. However, it may be that H. pylori infection is a surrogate marker for the 'hygiene hypothesis', a theory which postulates that early life infections are essential to prime the immune system and thus prevent allergic and autoimmune conditions later in life. The fact that the association between H. pylori seropositivity and MS risk was seen almost exclusively in females requires further investigation.

Actual and estimated adenoma detection rates: a 2‐year monocentric colonoscopic screening outcome in Shenzhen, China

Publisher: Wiley

Date: 16-03-2020

DOI: 10.1002/JGH3.12322

The redefinition of Helicobacter pylori lipopolysaccharide O-antigen and core-oligosaccharide domains

Publisher: Public Library of Science (PLoS)

Date: 17-03-2017

DOI: 10.1371/JOURNAL.PPAT.1006280

A re-testing range is recommended for 13C- and 14C-urea breath tests for Helicobacter pylori infection in China

Publisher: Springer Science and Business Media LLC

Date: 12-06-2021

DOI: 10.1186/S13099-021-00435-3

Abstract: The urea breath test (UBT) is widely used for diagnosing Helicobacter pylori infection. In the Shenzhen Kuichong People’s Hospital, some UBT findings were contradictory to the histology outcomes, therefore this study aimed to assess and compare the diagnostic performance of both 13 C- and 14 C-UBT assays. We recruited 484 H. pylori -treatment naïve patients, among which 217 and 267 were tested by the 13 C-UBT or 14 C-UBT, respectively. The cutoff value for H. pylori positivity based on manufacturer’s instruction was 4% delta over baseline (DOB) for the 13 C-UBT, and 100 disintegrations per minute (DPM) for the 14 C-UBT. Gastric biopsies of the antrum and corpus were obtained during endoscopy for histopathology. In patients who were tested using the 13 C-UBT kit, histopathology was positive in 136 out of 164 UBT-positive patients (82.9% concordance), and negative in 46 out of 53 UBT-negative cases (86.8% concordance). For the 14 C-UBT-tested patients, histopathology was positive for H. pylori in 186 out of 220 UBT-positive patients (84.5% concordance), and negative in 41 out of 47 UBT-negative cases (87.2% concordance). While the 13 C-UBT and 14 C-UBT each had a high sensitivity level of 95.1% and 96.9%, respectively, their specificity was low, at 62.2% and 54.7%, respectively. By using new optimal cutoff values and including an indeterminate range (3–10.3% DOB for 13 C-UBT and 87–237 DPM for 14 C-UBT), the specificity values can be improved to 76.7% and 76.9% for the 13 C- and 14 C-UBT, respectively. The establishment of an indeterminate range is recommended to allow for repeated testing to confirm H. pylori infection, and thereby avoiding unnecessary antibiotic treatment. Trial registration : Chinese Clinical Trial Registry, ChiCTR2000041570. Registered 29 December 2020- Retrospectively registered, www.chictr.org.cn/edit.aspx?pid=66416& htm=4

Editorial for Cancer Screening and Prevention

Publisher: Xia & He Publishing

Date: 09-03-2023

DOI: 10.14218/CSP.2023.00000

Susceptibility-guided bismuth quadruple therapies for resistant Helicobacter pylori infections

Publisher: Oxford University Press (OUP)

Date: 17-03-2020

DOI: 10.1093/PCMEDI/PBAA010

Abstract: Increasing Helicobacter pylori resistance to antibiotics has ledthat molecular testing is appropriate as a sub to adoption of seven different bismuth quadruple therapies (BQT) in China without differentiation of first-line or second-line regimens. The objective of this study was to evaluate the efficacy of susceptibility-guided BQT for patients who had experienced previous treatment failures. A total of 133 patients was included and H. pylori was successfully cultured from 101 patients (75.9%) for subsequent antimicrobial susceptibility testing (AST). Based on the AST results, 88 patients completed one of five AST-guided 14-day BQT regimens: esomeprazole and bismuth colloidal pectin, along with either, amoxicillin and clarithromycin (EBAC), amoxicillin and levofloxacin (EBAL), amoxicillin and furazolidone (EBAF), amoxicillin and tetracycline (EBAT), or tetracycline and furazolidone (EBTF). H. pylori eradication rates were 100% for EBAC (5/5), EBAL (13/13), EBAF (14/14), and EBTF (43/43), but 76.9% for EBAT (10/13). The three patients that failed the EBAT regimen were all cured after subsequent treatment with the EBTF regimen. Our study demonstrates the excellent efficacy of the AST-guided BQT for referred H. pylori patients, and that the current EBAT regimen, used in clinics, needs to be optimized. In addition, 57 of the isolates were subjected to whole-genome sequencing. Analysis of the sequences revealed that point mutations in 23S rRNA correlated well with the phenotypic clarithromycin resistance with a concordance of 91.2%, while the concordance between phenotypic levofloxacin resistance and gyrA point mutations was 82.3%. This suggests that molecular testing is appropriate as a substitute for AST as a more rapid and cost-effective method for determining clarithromycin and levofloxacin resistance in Chinese patients.

Helicobacter pylori VacA, a distinct toxin exerts diverse functionalities in numerous cells: An overview

Publisher: Wiley

Date: 16-10-2018

DOI: 10.1111/HEL.12544

Abstract: Helicobacter pylori, gastric cancer-causing bacteria, survive in their gastric environment of more than 50% of the world population. The presence of H. pylori in the gastric vicinity promotes the development of various diseases including peptic ulcer and gastric carcinoma. H. pylori produce and secret Vacuolating cytotoxin A (VacA), a major toxin facilitating the bacteria against the host defense system. The toxin causes multiple effects in epithelial cells and immune cells, especially T cells, B cells, and Macrophages. This review describes the erse functionalities of protein toxin VacA. The specific objective of this review is to address the overall structure, mechanism, and functions of VacA in various cell types. The recent advancements are summarized and discussed and thus conclusion is drawn based on the overall reported evidences. The searched articles on H. pylori VacA were evaluated and limited up to 66 articles for this review. The articles were ided into four major categories including articles on vacA gene, VacA toxin, distinct effects of VacA toxin, and their effects on various cells. Based on these studies, the review article was prepared. This review describes an overview of how VacA is secreted by H. pylori and contributes to colonization and virulence in multiple ways by affecting epithelial cells, T cells, Dendritic cells, B cells, and Macrophages. The reported evidence suggests that the comprehensive outlook need to be developed for understanding distinctive functionalities of VacA.

Epidemiology of Helicobacter in Chinese families: a foundation for cost-effective eradication strategies?

Publisher: BMJ

Date: 29-03-2023

DOI: 10.1136/GUTJNL-2023-329786

Need for standardization and harmonization of Helicobacter pylori antimicrobial susceptibility testing

Publisher: Wiley

Date: 12-02-2022

DOI: 10.1111/HEL.12873

Abstract: As with other infectious diseases, Helicobacter pylori eradication regimens should be guided by susceptibility testing to achieve excellent success rate, especially in the era of high antibiotic resistance. However, susceptibility testing for H. pylori is rarely performed, which can be partly ascribed to the current lack of standardization of testing methods and the lack of unified consensus on the antibiotic resistance breakpoints. The aim of this review was to call for an international consensus on standardization and harmonization of H. pylori susceptibility testing. We summarize and compare the advantages and disadvantages of four different phenotypic antimicrobial susceptibility testing (AST) methods (agar dilution, E‐test, disk diffusion, and broth microdilution) and the molecular susceptibility testing method for H. pylori . The standard phenotypic testing methods and the molecular testing methods have their own advantages and disadvantages. Compared to the standard phenotypic methods, the molecular testing method does not require successful H. pylori culture, and therefore, is much more rapid and convenient for clinical use. However, the currently available molecular testing method is only suitable for detecting clarithromycin and quinolone susceptibility profiles in H. pylori . Although the standard AST is time‐consuming, it is currently the only way to test the susceptibility of H. pylori to all the commonly used antibiotics. To make H. pylori susceptibility testing become a clinical routine, an international consensus on standardization and harmonization of H. pylori AST is needed. Future efforts are needed for optimizing broth culture of H. pylori , and developing commercial AST plates for achieving high throughput and automated susceptibility testing for H. pylori .

Primary antibiotic resistance of Helicobacter pylori among a Chinese Tibetan population

Publisher: Future Medicine Ltd

Date: 09-2020

DOI: 10.2217/FMB-2020-0206

Abstract: Aim: To evaluate the primary antibiotic resistance in Helicobacter pylori strains isolated from a Chinese Tibetan population. Methods & materials: Gastric biopsies from 400 H. pylori treatment-naive Tibetan patients were collected for H. pylori isolation. Susceptibility to amoxicillin (AML)/clarithromycin (CLR)/levofloxacin (LEV)/metronidazole (MTZ)/tetracycline (TET)/rif icin (RIF)/furazolidone (FZD) was determined by E-test or a disk diffusion assay. Results: Biopsies from 117 patients were H. pylori culture positive (29.3%). The primary resistance rates to MTZ, CLR, LEV, RIF, AML, TET and FZD were 90.6, 44.4, 28.2, 69.2, 7.7, 0.8 and 0.8%, respectively. Interestingly, 42.7% of the strains had simultaneous resistance to CLR and MTZ. Conclusion: Among Tibetan strains, primary resistance rates were high for CLR/MTZ/LEV, whereas primary resistance rates to AML/TET/FZD were low. The high resistance to RIF is a concerning finding.

Sequential fractionation of the lignocellulosic components in hardwood based on steam explosion and hydrotropic extraction

Publisher: Springer Science and Business Media LLC

Date: 04-01-2019

DOI: 10.1186/S13068-018-1346-Y

Elucidation of Changes in Cellulose Ultrastructure and Accessibility in Hardwood Fractionation Processes with Carbohydrate Binding Modules

Publisher: American Chemical Society (ACS)

Date: 31-03-2020

DOI: 10.1021/ACSSUSCHEMENG.9B07589

Mutations of Helicobacter pylori RdxA are mainly related to the phylogenetic origin of the strain and not to metronidazole resistance

Publisher: Oxford University Press (OUP)

Date: 17-07-2020

DOI: 10.1093/JAC/DKAA302

Abstract: Drug resistance of Helicobacter pylori is a major clinical problem worldwide. The objective of the present study was to investigate the prevalence of antibiotic-resistant H. pylori in the city of Shenzhen in China, as well as to identify the genetic mutations specifically associated with drug resistance rather than unrelated phylogenetic signals. Antibiotic susceptibility testing was performed on 238 clinical strains successfully isolated from H. pylori-positive dyspeptic patients who underwent gastroscopy at the Department of Gastroenterology in Shenzhen People’s Second Hospital. Following WGS of all strains using Illumina technology, mutation and phylogenetic analyses were performed. The resistance rates were 84.9%, 35.3%, 25.2% and 2.1% for metronidazole, clarithromycin, ciprofloxacin and rif icin, respectively. An A2143G conversion in the 23S rRNA gene was the primary mutation observed in clarithromycin-resistant strains, whilst N87K/I and D91G/N/Y in GyrA were detected in ciprofloxacin-resistant strains. In RdxA, our results demonstrated that only R16H/C and M21A are significant contributors to metronidazole resistance there were 15 other sites, but these are phylogenetically related and thus unrelated to metronidazole resistance. There is a high prevalence of metronidazole, clarithromycin and ciprofloxacin resistance and a low prevalence of rif icin resistance in H. pylori from Shenzhen, China. Omission of phylogenetically related sites will help to improve identification of sites genuinely related to antibiotic resistance in H. pylori and, we believe, other species.

The Peopling of the Pacific from a Bacterial Perspective

Publisher: American Association for the Advancement of Science (AAAS)

Date: 23-01-2009

DOI: 10.1126/SCIENCE.1166083

Abstract: Two prehistoric migrations peopled the Pacific. One reached New Guinea and Australia, and a second, more recent, migration extended through Melanesia and from there to the Polynesian islands. These migrations were accompanied by two distinct populations of the specific human pathogen Helicobacter pylori , called hpSahul and hspMaori, respectively. hpSahul split from Asian populations of H. pylori 31,000 to 37,000 years ago, in concordance with archaeological history. The hpSahul populations in New Guinea and Australia have erged sufficiently to indicate that they have remained isolated for the past 23,000 to 32,000 years. The second human expansion from Taiwan 5000 years ago dispersed one of several subgroups of the Austronesian language family along with one of several hspMaori clades into Melanesia and Polynesia, where both language and parasite have continued to erge.

Development of a bowel sound detector adapted to demonstrate the effect of food intake

Publisher: Springer Science and Business Media LLC

Date: 04-01-2022

DOI: 10.1186/S12938-021-00969-2

Abstract: Bowel sounds (BS) carry useful information about gastrointestinal condition and feeding status. Interest in computerized bowel sound-based analysis has grown recently and techniques have evolved rapidly. An important first step for these analyses is to extract BS segments, whilst neglecting silent periods. The purpose of this study was to develop a convolutional neural network-based BS detector able to detect all types of BS with accurate time st s, and to investigate the effect of food consumption on some acoustic features of BS with the proposed detector. Audio recordings from 40 volunteers were collected and a BS dataset consisting of 6700 manually labelled segments was generated for training and testing the proposed BS detector. The detector attained 91.06% and 90.78% accuracy for the validation dataset and across-subject test dataset, respectively, with a well-balanced sensitivity and specificity. The detection rates evaluated on different BS types were also satisfactory. Four acoustic features were evaluated to investigate the food effect. The total duration and spectral bandwidth of BS showed significant differences before and after food consumption, while no significant difference was observed in mean-crossing rate values. We demonstrated that the proposed BS detector is effective in detecting all types of BS, and providing an accurate time st for each BS. The characteristics of BS types and the effect on detection accuracy is discussed. The proposed detector could have clinical application for post-operative ileus prognosis, and monitoring of food intake.

A novel taxon selection method, aimed at minimizing recombination, clarifies the discovery of a new sub‐population of Helicobacter pylori from Australia

Publisher: Wiley

Date: 18-09-2019

DOI: 10.1111/EVA.12864

A mathematical model of bowel sound generation

Publisher: Acoustical Society of America (ASA)

Date: 12-2018

DOI: 10.1121/1.5080528

Abstract: Humans have been interested in bowel sounds and wondered about their origins for millennia. To better understand the phenomenon, a mathematical model of bowel sound generation was developed based on a spring-mass-d ing system. This is similar to vocal folds models for speech. The bowel sound model has four parameters that link to bowel activities: the in idual wave component, pressure index, component quantity, and component interval time. All types of bowel sound documented previously can be modelled by combining different values for these parameters. Further, a 2500 ms bowel sound incorporating all the common types was simulated to present the model's accuracy.

University Of Western Australia

Location: Australia

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Lund University

Location: Sweden

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Linkage Infrastructure, Equipment And Facilities - Grant ID: LE100100217

Start Date: 2010

End Date: 05-2011

Amount: $450,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0989782

Start Date: 10-2009

End Date: 10-2010

Amount: $524,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE130100126

Start Date: 2013

End Date: 12-2013

Amount: $160,000.00

Funder: Australian Research Council