<i>Gut Pathogens</i>: enteric health at the interface of changing microbiology

The International Society for Genomic and Evolutionary Microbiology (ISOGEM) in collaboration with BioMed Central Ltd. has launched Gut Pathogens with the aim of providing a high-quality forum for research on enteric infections of humans and animals. The journal led by three Editors-in-Chief and supported by a highly qualified and organized international Editorial Board publishes open access research articles of repute in areas of biology and the pathogenesis of bacterial, parasitic and viral infections of the gut including their diagnosis, epidemiology and clinical management

DPO multiplex PCR as an alternative to culture and susceptibility testing to detect Helicobacter pylori and its resistance to clarithromycin

<p>Abstract</p> <p>Background</p> <p>Macrolide resistance in <it>Helicobacter pylori </it>is the major risk factor for treatment failure when using a proton pump inhibitor-clarithromycin containing therapy. Macrolide resistance is due to a few mutations on the 23S ribomosal subunit encoded by the 23S rRNA gene. The present study aimed at investigating the performance of the dual priming oligonucleotide (DPO)-PCR kit named Seeplex^®ClaR-<it>H. pylori </it>ACE detection designed to detect <it>H. pylori </it>and two types of point mutations causing clarithromycin resistance in <it>H. pylori</it>.</p> <p>Methods</p> <p>The performance of Seeplex^®ClaR-<it>H. pylori </it>ACE detection was evaluated on 127 gastric biopsies in comparison to conventional bacterial culture followed by the determination of susceptibility to clarithromycin by E-test, as well as by an in-house real-time PCR using a fluorescence resonance energy transfer (FRET) technology.</p> <p>Results</p> <p>Considering culture as the reference test, the sensitivity of DPO-PCR and real-time FRET-PCR was 97.7% and 100% while specificity was 83.1% and 80.7%, respectively. However, both PCR were concordant in detecting 14 <it>H. pylori </it>positive cases which were negative by culture. Globally, E-test and DPO-PCR were concordant with regard to clarithromycin susceptibility in 95.3% of the cases (41/43), while real-time FRET-PCR and DPO-PCR were concordant in 95% (57/60).</p> <p>Conclusion</p> <p>The DPO-PCR is an interesting tool to detect <it>H. pylori </it>on gastric biopsies and to study its susceptibility to clarithromycin in laboratories that cannot perform real-time PCR assays.</p

Campylobacter infections in human : results of threeyears of surveillance 2001 - 2003

The frequency of Campylobacter infections in human, their potential severity, and the existence of preventive measures warrant the creation of a surveillance system. A Campylobacter surveillance system based on private laboratories (PL) was set up in France in 2002 to complement the hospital laboratory-based system(HL). Since 1 January 2001 (for HL), 1 April 2002 (for PL) and 31 December 2003, the Campylobacter National reference Centre analyzed 3 698 strains. Initially thought to be 3.4/100,000, the overall isolation rate was grossly underestimated, as the latest figure is 14/100,000 among children under 5 years old. The strains were mainly C. jejuni (76.9%), followed by C. coli (17.0%) and C. fetus (5.4%). Resistance rates were 41% for ampicillin and 28% for nalidixic acid. Surveillance must be maintained to collect more data on Campylobacter epidemiology in France and to estimate its incidence in the general population.La fréquence des infections humaines à Campylobacter, leur gravité potentielle et l'existence de mesures de prévention justifient une surveillance. En France, un système de surveillance des infections à Campylobacter a été mis en place en avril 2002, à partir des laboratoires de ville (LABM), en complément de celui du réseau des laboratoires hospitaliers (LH) existant depuis 1986. Entre le 1/01/01 (pour les LH), le 1/04/02 (pour les LABM) et le 31/12/03, le Centre National de Référence des Campylobacter a expertisé 3698 souches. Le taux global d'isolement de 3,4/100000 était très largement sous-estimé : il était de 14/100000 pour les enfants âgés de moins S ans. C. jejuni représentait 76,9% des souches, suivi de C. coli (17,0 %) et de C. fetus (5,4%). Le taux de résistance à l'ampicilline était de 41 % et à l'acide nalidixique de 28%. Les efforts pour la surveillance doivent être poursuivis, afin de mieux connaître les caractéristiques épidémiotogiques des infection à Campylobacter en France et de faire des estimations d'incidence en population générale

Joint ESPGHAN/NASPGHAN Guidelines for the Management of Helicobacter pylori in Children and Adolescents ( Update 2016)

Background: Because of the changing epidemiology of Helicobacter pylori infection and low efficacy of currently recommended therapies, an update of the European Society for Paediatric Gastroenterology Hepatology and Nutrition/North American Society for Pediatric Gastroenterology, Hepatology and Nutrition recommendations for the diagnosis and management of H pylori infection in children and adolescents is required. Methods: Asystematic review of the literature (time period: 2009-2014) was performed. Representatives of both societies evaluated the quality of evidence using GRADE (Grading of Recommendation Assessment, Development, and Evaluation) to formulate recommendations, which were voted upon and finalized using a Delphi process and face-to-face meeting. Results: The consensus group recommended that invasive diagnostic testing for Hpylori be performed only when treatment will be offered if tests are positive. To reach the aim of a 90% eradication rate with initial therapy, antibiotics should be tailored according to susceptibility testing. Therapy should be administered for 14 days, emphasizing strict adherence. Clarithromycin-containing regimens should be restricted to children infected with susceptible strains. When antibiotic susceptibility profiles are not known, high-dose triple therapy with proton pump inhibitor, amoxicillin, and metronidazole for 14 days or bismuth-based quadruple therapy is recommended. Success of therapy should be monitored after 4 to 8 weeks by reliable noninvasive tests. Conclusions: The primary goal of clinical investigation is to identify the cause of upper gastrointestinal symptoms rather than H pylori infection. Therefore, we recommend against a test and treat strategy. Decreasing eradication rates with previously recommended treatments call for changes to first-line therapies and broader availability of culture or molecular-based testing to tailor treatment to the individual child

Who Could Be Blamed in the Case of Discrepant Histology and Serology Results for Helicobacter pylori Detection?

Funding Information: Acknowledgments: The study was funded in part by the Fundamental and Applied Research Project Program in Latvia, project No. lzp-2018/1-0135 “Research on implementation of a set of measures for prevention of gastric cancer mortality by eradication H. pylori and timely recognition of precancerous lesions”. We acknowledge the entire GISTAR study team as well as the infrastructure provided by the Digestive Diseases Centre GASTRO for endoscopy and the Academic Histology Laboratory for pathology infrastructures. Our acknowledgements also to Biohit Oyj, Finland, for their support with laboratory reagents. Funding Information: Funding: The work is funded by ERDF (European Regional Development Fund) within the frame-work of 2nd part of measure 1.1.1.1. ‘Practical Studies’, project ID Nr. 1.1.1.1/18/A/184. Funding Information: The work is funded by ERDF (European Regional Development Fund) within the framework of 2nd part of measure 1.1.1.1. ?Practical Studies?, project ID Nr. 1.1.1.1/18/A/184. Publisher Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland.Background. Discrepancies between histology and serology results for Helicobacter pylori detection could be caused by a variety of factors, including a biopsy sampling error, expertise of the pathologist, natural loss of infection due to advanced atrophy, or a false-positive serology in the case of a previous infection, since antibodies may be present in blood following recovery from the infection. Aims. To identify true H. pylori-positive individuals in discrepant cases by serology and histology using real time polymerase chain reaction (RT-PCR) as a gold standard. Methods. Study subjects with discrepant histology and serology results were selected from the GISTAR pilot study data base in Latvia. Subjects having received previous H. pylori eradication therapy or reporting use of proton pump inhibitors, antibacterial medications, or bismuth containing drugs one month prior to upper endoscopy were excluded. We compared the discrepant cases to the corresponding results of RT-PCR performed on gastric biopsies. Results. In total, 97 individuals with discrepant results were identified: 81 subjects were serology-positive/histology-negative, while 16 were serologynegative/histology-positive. Among the serology-positive/histology-negative cases, 64/81 (79.0%) were false-positives by serology and, for the majority, inflammation was absent in all biopsies, while, in the serology-negative/histology-positive group, only 6.2% were proven false-positives by histology. Conclusions. Among this high H. pylori prevalent, middle-aged population, the majority of discrepant cases between serology and histology were due to false positive-serology, rather than false-negative histology. This confirms the available evidence that the choice of treatment should not be based solely on the serological results, but also after excluding previous, self-reported eradication therapy.publishersversionPeer reviewe

A standardised model for stool banking for faecal microbiota transplantation : a consensus report from a multidisciplinary UEG working group

Background Faecal microbiota transplantation is an emerging therapeutic option, particularly for the treatment of recurrent Clostridioides difficile infection. Stool banks that organise recruitment and screening of faeces donors are being embedded within the regulatory frameworks described in the European Union Tissue and Cells Directive and the technical guide to the quality and safety of tissue and cells for human application, published by the European Council. Objective Several European and international consensus statements concerning faecal microbiota transplantation have been issued. While these documents provide overall guidance, we aim to provide a detailed description of all processes that relate to the collection, handling and clinical application of human donor stool in this document. Methods Collaborative subgroups of experts on stool banking drafted concepts for all domains pertaining to stool banking. During a working group meeting in the United European Gastroenterology Week 2019 in Barcelona, these concepts were discussed and finalised to be included in our overall guidance document about faecal microbiota transplantation. Results A guidance document for all domains pertaining to stool banking was created. This document includes standard operating manuals for several processes involved with stool banking, such as handling of donor material, storage and donor screening. Conclusion The implementation of faecal microbiota transplantation by stool banks in concordance with our guidance document will enable quality assurance and guarantee the availability of donor faeces preparations for patients.Peer reviewe

European Registry on Helicobacter pylori Management: Effectiveness of First and Second-Line Treatment in Spain

The management of Helicobacter pylori infection has to rely on previous local effectiveness due to the geographical variability of antibiotic resistance. The aim of this study was to evaluate the effectiveness of first and second-line H. pylori treatment in Spain, where the empirical prescription is recommended. A multicentre prospective non-interventional registry of the clinical practice of European gastroenterologists concerning H. pylori infection (Hp-EuReg) was developed, including patients from 2013 until June 2019. Effectiveness was evaluated descriptively and through a multivariate analysis concerning age, gender, presence of ulcer, proton-pump inhibitor (PPI) dose, therapy duration and compliance. Overall, 53 Spanish hospitals were included, and 10,267 patients received a first-line therapy. The best results were obtained with the 10-day bismuth single-capsule therapy (95% cure rate by intention-to-treat) and with both the 14-day bismuth-clarithromycin quadruple (PPI-bismuth-clarithromycin-amoxicillin, 91%) and the 14-day non-bismuth quadruple concomitant (PPI-clarithromycin-amoxicillin-metronidazole, 92%) therapies. Second-line therapies were prescribed to 2448 patients, with most-effective therapies being the triple quinolone (PPI-amoxicillin-levofloxacin/moxifloxacin) and the bismuth-levofloxacin quadruple schemes (PPI-bismuth-levofloxacin-amoxicillin) prescribed for 14 days (92%, 89% and 90% effectiveness, respectively), and the bismuth single-capsule (10 days, 88.5%). Compliance, longer duration and higher acid inhibition were associated with higher effectiveness. "Optimized" H. pylori therapies achieve over 90% success in Spain

Effectiveness of empirical <i>Helicobacter pylori</i> eradication therapy with furazolidone in Russia: results from the European Registry on <i>Helicobacter pylori</i> Management (Hp-EuReg)

Background. First-line therapy does not always provide a high level of Helicobacter pylori eradication due to the increase of H. pylori resistance to antibiotics; therefore, it remains necessary to identify the most effective rescue treatments. The purpose of this study was to evaluate the efficacy and safety of empirical H. pylori furazolidone-containing regimens. Materials and methods. Adult H. pylori infected patients empirically treated with furazolidone-containing eradication regimens were registered in an international, prospective, multicenter non-intervention European registry on H. pylori management (Hp-EuReg). Data were collected at AEG-REDCap e-CRF from 2013 to 2021 and the quality was reviewed. Modified intention-to-treat (mITT) effectiveness analyses were performed. Results. Overall 106 patients received empirical furazolidone-containing therapy in Russia. Furazolidone was prescribed in a sequential scheme along with amoxicillin, clarithromycin and a proton pump inhibitor in 68 (64%) cases, triple regimens were prescribed in 28 (26%) patients and quadruple regimens in 10 (9.4%). Treatment duration of 7 days was assigned to 2 (1.9%) patients, 10-day eradication therapy in case of 80 (75%) and 14 days in 24 (23%) patients. Furazolidone was mainly used in first- (79%) and second-line (21%) regimens. The methods used to diagnose H. pylori infection were: histology (81%), stool antigen test (64%), 13C-urea breath test (6.6%), and rapid urease test (1.9%). The mITT effectiveness of sequential therapy was 100%; 93% with the triple therapy and 75.5% with quadruple therapy. Compliance was reported in 98% of cases. Adverse events were revealed in 5.7% of patients, mostly nausea (3.8%). No serious adverse events were reported. Conclusion. Furazolidone containing eradication regimens appear to be an effective and safe empirical therapy in Russia

The Helicobacter pylori Genome Project : insights into H. pylori population structure from analysis of a worldwide collection of complete genomes

Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics

Contribution à l' étude des souches de Helicobacter pylori associées au lymphome gastrique du MALT de faible degré de malignité

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