The second Irish Helicobacter pylori Working Group consensus for the diagnosis and treatment of Helicobacter pylori infection in adult patients in Ireland.

BACKGROUND: There has been an increase in resistance to many of the antimicrobials used to treat Helicobacter pylori (H. pylori) nationally and internationally. Primary clarithromycin resistance and dual clarithromycin and metronidazole resistance are high in Ireland. These trends call for an evaluation of best-practice management strategies. OBJECTIVE: The objective of this study was to revise the recommendations for the management of H. pylori infection in adult patients in the Irish healthcare setting. METHODS: The Irish H. pylori working group (IHPWG) was established in 2016 and reconvened in 2023 to evaluate the most up-to-date literature on H. pylori diagnosis, eradication rates and antimicrobial resistance. The 'GRADE' approach was then used to rate the quality of available evidence and grade the resulting recommendations. RESULTS: The Irish H. pylori working group agreed on 14 consensus statements. Key recommendations include (1) routine antimicrobial susceptibility testing to guide therapy is no longer recommended other than for clarithromycin susceptibility testing for first-line treatment (statements 6 and 9), (2) clarithromycin triple therapy should only be prescribed as first-line therapy in cases where clarithromycin susceptibility has been confirmed (statement 9), (3) bismuth quadruple therapy (proton pump inhibitor, bismuth, metronidazole, tetracycline) is the recommended first-line therapy if clarithromycin resistance is unknown or confirmed (statement 10), (4) bismuth quadruple therapy with a proton pump inhibitor, levofloxacin and amoxicillin is the recommended second-line treatment (statement 11) and (5) rifabutin amoxicillin triple therapy is the recommend rescue therapy (statement 12). CONCLUSION: These recommendations are intended to provide the most relevant current best-practice guidelines for the management of H. pylori infection in adults in Ireland.

A geographic cluster of healthcare-associated carbapenemase-producing hypervirulent Klebsiella pneumoniae sequence type 23.

Hypervirulent Klebsiella pneumoniae has typically been associated with invasive, community-associated infections. This study describes the molecular, epidemiological and clinical characteristics of a cluster of carbapenemase-producing hypervirulent K. pneumoniae in the South-East of Ireland. It highlights the increasing risk that hypervirulent K. pneumoniae poses to healthcare and residential care populations. A retrospective analysis of sequences on K. pneumoniae isolates in the K. pneumoniae database of the National Carbapenemase-Producing Enterobacterales Reference Laboratory Service was performed to identify cases of hypervirulent K. pneumoniae from one hospital network. Hypervirulence scores were assigned based on the presence of recognised hypervirulence genes. A retrospective review of patient records was carried out for all confirmed cases of hypervirulent K. pneumoniae identified and clinical, epidemiological and molecular characteristics described. Twenty-eight cases of hypervirulent OXA-48 producing K. pneumoniae were identified over a 2-year period. All isolates were sequence-type 23 with a hypervirulence score of 5. All isolates carried the blaOXA-48 carbapenemase gene. All cases had a record of current or recent hospitalisation or residence in a long-term residential care facility. This study describes extensive dissemination of hypervirulent K. pneumoniae within healthcare facilities and an ongoing outbreak in our region. It shows the convergence of hypervirulence and antibiotic resistance determinants. Healthcare facilities need to consider their infection prevention, control and surveillance strategies to monitor and prevent further dissemination among a vulnerable population. Diagnostic laboratories need to ensure they have the ability and capacity for testing. Readily deployed laboratory methods for detection of hypervirulence are required.

A compact instrument for gamma-ray burst detection on a CubeSat platform II: Detailed design, assembly and validation.

The Gamma-ray Module, GMOD, is a miniaturised novel gamma-ray detector which will be the primary scientific payload on the Educational Irish Research Satellite (EIRSAT-1) 2U CubeSat mission. GMOD comprises a compact (25 mm × 25 mm × 40 mm) cerium bromide scintillator coupled to a tiled array of 4 × 4 silicon photomultipliers, with front-end readout provided by the IDE3380 SIPHRA. This paper presents the detailed GMOD design and the accommodation of the instrument within the restrictive CubeSat form factor. The electronic and mechanical interfaces are compatible with many off-the-shelf CubeSat systems and structures. The energy response of the GMOD engineering qualification model has been determined using radioactive sources, and an energy resolution of 5.4% at 662 keV has been measured. EIRSAT-1 will perform on-board processing of GMOD data. Trigger results, including light-curves and spectra, will be incorporated into the spacecraft beacon and transmitted continuously. Inexpensive hardware can be used to decode the beacon signal, making the data accessible to a wide community. GMOD will have scientific capability for the detection of gamma-ray bursts, in addition to the educational and technology demonstration goals of the EIRSAT-1 mission. The detailed design and measurements to date demonstrate the capability of GMOD in low Earth orbit, the scalability of the design for larger CubeSats and as an element of future large gamma-ray missions.

A compact instrument for gamma-ray burst detection on a CubeSat platform I: Design drivers and expected performance.

The Educational Irish Research Satellite 1 (EIRSAT-1) is a 2U CubeSat being developed under ESA's Fly Your Satellite! programme. The project has many aspects, which are primarily educational, but also include space qualification of new detector technologies for gamma-ray astronomy and the detection of gamma-ray bursts (GRBs). The Gamma-ray Module (GMOD), the main mission payload, is a small gamma-ray spectrometer comprising a 25 mm × 25 mm × 40 mm cerium bromide scintillator coupled to an array of 16 silicon photomultipliers. The readout is provided by IDE3380 (SIPHRA), a low-power and radiation tolerant readout ASIC. GMOD will detect gamma-rays and measure their energies in a range from tens of keV to a few MeV. Monte Carlo simulations were performed using the Medium Energy Gamma-ray Astronomy Library to evaluate GMOD's capability for the detection of GRBs in low Earth orbit. The simulations used a detailed mass model of the full spacecraft derived from a very high-fidelity 3D CAD model. The sky-average effective area of GMOD on board EIRSAT-1 was found to be 10 cm2 at 120 keV. The instrument is expected to detect between 11 and 14 GRBs, at a significance greater than 10σ (and up to 32 at 5σ), during a nominal one-year mission. The shape of the scintillator in GMOD results in omni-directional sensitivity which allows for a nearly all-sky field of view.

Specialist training in medical microbiology across Europe in 2021-an update on the actual training situation based on a survey.

BACKGROUND: The importance of defining and establishing professional standards for Clinical Microbiology (CM) in Europe has long been highlighted, starting with the development of a European curriculum. The first European Curriculum in Medical Microbiology (MM) was adopted by the European Union of Medical Specialists (UEMS) council in 2017. OBJECTIVES: This paper assesses how training programmes in CM in Europe align with the European curriculum, just under 5 years after its introduction, and reviews what methods of assessment are in use to assess the CM trainees' progress during training programmes. SOURCES: Using an internet-based platform, a questionnaire was circulated to the full, associate and observer members of the UEMS MM section. Information collected related to the structure, content and delivery of CM training in the participating countries, as well as methods of assessment used to evaluate training progress. CONTENT: Twenty-one countries responded, from a total of 30 countries invited to participate. All had a structured CM training programme, with a curriculum, dedicated trainers and a record of training activities. Fifteen countries require trainees to pass an exit examination, and over 60% of countries participate in continuous workplace-based assessment. Of the participating countries, 57% meet the European Training Requirements recommendation that duration of specialist training is 60 months. Regarding core competencies, all trainees gain experience in laboratory skills and infection prevention and control, but the emphasis on clinical management and antimicrobial stewardship is more varied across countries. IMPLICATIONS: The UEMS MM curriculum has been largely adopted by 21 countries within less than 5 years of ratification, which speaks optimistically to a future of standardized quality training across Europe. The introduction of a pilot European Examination in Clinical Microbiology in 2021 is the start of a pan-European assessment of the success of the implementation of this curriculum and the first step in quality assurance for CM training in Europe.

Psychological impact of the COVID-19 pandemic on healthcare workers at acute hospital settings in the South-East of Ireland: an observational cohort multicentre study.

OBJECTIVE: Our study aims to understand the psychological impact of the COVID-19 pandemic among healthcare workers (HCWs) at acute hospital settings in the South-East of Ireland, as a crucial step in guiding policies and interventions to maintain their psychological well-being. DESIGN: Observational cohort study. PARTICIPANTS AND SETTING: 472 HCWs participated from two distinct acute hospital settings, A and B, in the South-East of Ireland. PRIMARY AND SECONDARY OUTCOME MEASURES: Measures of psychological distress-depression, anxiety, acute and post-traumatic stress disorder (PTSD)-as dictated by the Depression, Anxiety and Stress Scale (DASS-21) and Impact of Event Scale-Revised (IES-R). An independent sample t-test and a Mann-Whitney U test was used to determine significance of difference in continuous variables between groups. Categorical variables were assessed for significance with a χ2 test for independence. RESULTS: The DASS-21 provided independent measures of depression (mean 4.57, IQR 2-7), anxiety (mean 3.87, IQR 1-6) and stress (mean 7.41, IQR 4-10). Positive scores were reflected in 201 workers (42.6%) for depression and 213 (45.1%) for both anxiety and stress. The IES-R measured subjective distress on three subscales: intrusion (mean 1.085, IQR 0.375-1.72), avoidance (mean 1.008, IQR 0.375-1.5) and hyperarousal (mean 1.084, IQR 0.5-1.667). Overall, 195 cases (41.3%) were concerning for PTSD. Site B scored significantly higher across all parameters of depression (5.24 vs 4.08, p<0.01), anxiety (4.66 vs 3.3, p<0.01), stress (8.91 vs 6.33, p<0.01) and PTSD (0.058 vs 0.043, p<0.01). Worse outcomes were also noted in HCWs with underlying medical ailments. CONCLUSION: Psychological distress is prevalent among HCWs during the COVID-19 pandemic; screening for adverse mental and emotional outcomes and developing timely tailored preventative measures with effective feedback are vital to protect their psychological well-being, both in the immediate and long-term.

Preventing sepsis development in complicated urinary tract infections.

Introduction: Urinary tract infections (UTIs) are the most prevalent infections in the community and the most common reason for antimicrobial prescribing in ambulatory care. A UTI is defined as complicated when urinary tract anatomical abnormalities or urinary devices are present, when it is recurrent and when associated with immunodeficiency. Complicated UTIs (cUTIs) have a higher risk of treatment failure and often require longer antimicrobial treatment courses. cUTIs, especially those which are healthcare-associated, are often due to multidrug resistant organisms (MDROs).Areas covered: This article will review the available evidence in relation to prevention of sepsis in cUTI, evaluating the risk factors associated with sepsis development. Published articles from January 2005 to September 2019 on UTIs and sepsis prevention in complicated UTIs were identified by using MEDLINE (National Library of Medicine Bethesda MD) and by reviewing the references of retrieved articles.Expert opinion: Prevention of sepsis relies on prompt and timely diagnosis of cUTI, early identification of the causative organism, removal of obstructions and source control, proper and adequate empirical/targeted antimicrobial treatment. In particular, source control, i.e. removal of urinary obstructions, infected stents, urinary catheters, nephrostomies, and drainage of hydronephrosis/abscess, is essential for preventing the development and progression of sepsis.

Epididymo-orchitis caused by enteric organisms in men > 35 years old: beyond fluoroquinolones.

Epididymo-orchitis is a common urological condition in men of all ages, causing a unilateral or bilateral swelling of the epididymis and/or testis. It is frequently caused by sexually transmitted infections, Chlamydia trachomatis and Neisseria gonorrheae, as well as common enteric organisms implicated in urinary tract infections. Men over 35 years old may develop epididymo-orchitis associated with enteric organisms, often associated with functional bladder outlet problems such as benign prostatic hyperplasia or urethral stricture disease. Fluoroquinolones, especially ciprofloxacin, have long been the mainstay of treatment for these infections; however, rising resistance to ciprofloxacin in E. coli isolates in Europe and the USA means that there is an unprecedented necessity for alternative antimicrobials with adequate penetration into genital tissues (epididymis and testes) to allow appropriate and comprehensive treatment of epididymo-orchitis in this group of patients.

A 2-year comparative study of mold and bacterial counts in air samples from neutral and positive pressure rooms in 2 tertiary care hospitals.

Immunocompromised patients are at risk of invasive fungal infection. These high-risk patients are nursed in protective isolation to reduce the risk of nosocomial aspergillosis while in hospital-ideally in a positive pressure single room with high-efficiency particulate air filtration. However, neutral pressure rooms are a potential alternative, especially for patients requiring both protective and source isolation. This study examined mold and bacterial concentrations in air samples from positive and neutral pressure rooms to assess whether neutral pressure rooms offer a similar environment to that of positive pressure rooms in terms of mold concentrations in the air. Mold concentrations were found to be similar in the positive and neutral pressure room types examined in this study. These results add to the paucity of literature in this area.

Aeromonas species endogenous endophthalmitis.

INTRODUCTION: Aeromonas spp. are Gram-negative bacteria classically associated with water sources and a variety of clinical infections in humans. CASE PRESENTATION: A 79-year-old female patient presented with gastroenteritis with associated Aeromonas spp. bloodstream infection. Two days after admission she developed eye symptoms and was diagnosed with endophthalmitis and underwent emergency evisceration and implant. Aeromonas spp. was also recovered from intra-ocular samples. CONCLUSION: In this case gastroenteritis caused by Aeromonas spp. was complicated by bloodstream infection which seeded to the eye, resulting in rapidly progressive endogenous endophthalmitis.

The Irish Helicobacter pylori Working Group consensus for the diagnosis and treatment of H. pylori infection in adult patients in Ireland.

BACKGROUND: Irish eradication rates for Helicobacter pylori are decreasing and there is an increase in the prevalence of antibiotic-resistant bacteria. These trends call into question current management strategies. OBJECTIVE: To establish an Irish Helicobacter pylori Working Group (IHPWG) to assess, revise and tailor current available recommendations. METHODS: Experts in the areas of gastroenterology and microbiology were invited to join the IHPWG. Questions of relevance to diagnosis, first-line and rescue therapy were developed using the PICO system. A literature search was performed. The 'Grading of Recommendations Assessment, Development and Evaluation' approach was then used to rate the quality of available evidence and grade the resulting recommendations. RESULTS: Key resultant IHPWG statements (S), the strength of recommendation and quality of evidence include S8: standard triple therapy for 7 days' duration can no longer be recommended (strong and moderate). S9: 14 days of clarithromycin-based triple therapy with a high-dose proton pump inhibitor (PPI) is recommended as first-line therapy. Bismuth quadruple therapy for 14 days is an alternative if available (strong and moderate). S12: second-line therapy depends on the first-line treatment and should not be the same treatment. The options are (a) 14 days of levofloxacin-based therapy with high-dose PPI, (b) 14 days of clarithromycin-based triple therapy with high-dose PPI or (c) bismuth quadruple therapy for 14 days (strong and moderate). S13: culture and antimicrobial susceptibility testing should be performed following two treatment failures (weak and low/very low). CONCLUSION: These recommendations are intended to provide the most relevant current best-practice guidelines for the management of H. pylori infection in adults in Ireland.

Matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometry (MS) for the identification of mycobacteria from MBBacT ALERT 3D liquid cultures and Lowenstein-Jensen (LJ) solid cultures.

AIMS: Conventional methods for the identification of mycobacteria can be demanding and prolonged. Molecular methodologies, although rapid, are expensive and often exclusive to reference laboratories. Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) presents a possible alternative method for the identification and differentiation of mycobacteria. This study describes the design and validation of a mycobacteria inactivation protocol and subsequent evaluation of MALDI-TOF MS for the identification of mycobacteria in a clinical microbiology laboratory setting. METHODS: A total of 65 non-tuberculous mycobacteria (NTM) isolates and 86 Mycobacterium tuberculosis complex (MTC) isolates were tested on the Bruker MALDI Biotyper Microflex, V.3.1. NTM solid-culture (Lowenstein-Jensen, LJ slopes) isolates (n=21) and liquid-culture (MBBacT ALERT 3D bottles) isolates (n=44) were tested. MTC solid-culture isolates (n=30) and liquid-culture isolates (n=56) were also tested. Isolates were subjected to the validated inactivation protocol and analysed on the MALDI-TOF MS instrument. RESULTS: The inactivation protocol designed was successfully validated and applied to all test isolates. MALDI-TOF MS correctly identified 82.8% of all isolates analysed; 96.7% and 96.4% of MTC isolates and 76.2% and 52.3% of NTM isolates were successfully identified from solid and liquid culture, respectively. MALDI-TOF MS failed to identify 35.4% (n=23) of NTM isolates and 3.5% (n=3) of MTC isolates. CONCLUSIONS: MALDI-TOF MS has potential for identifying mycobacteria in the clinical laboratory setting, by reducing identification turnaround time and laboratory costs in isolate referral. Isolates that failed to be identified are explained by limitations of the method.

False extended-spectrum {beta}-lactamase phenotype in clinical isolates of Escherichia coli associated with increased expression of OXA-1 or TEM-1 penicillinases and loss of porins.

OBJECTIVES: Two clinical isolates of Escherichia coli, EC18 and EC21, were non-susceptible (MICs 4-16 mg/L) to cefpirome and cefepime, with marked synergy with clavulanate, yet were susceptible to cefotaxime and ceftazidime (MICs ≤ 1 mg/L). EC19, from the same patient as EC21, was susceptible to all four cephalosporins. We sought to characterize the molecular basis of resistance in isolates EC18 and EC21. METHODS: PFGE was used to study the genetic relationships of the isolates, and MICs were determined. ß-Lactamases were characterized by PCR, isoelectric focusing (IEF), construction of genomic libraries and sequencing. A double mutant of E. coli J53 was constructed, lacking OmpC and OmpF porins. Plasmids from clinical isolates were transformed into E. coli J53 and J53ΔompCF. Outer membrane proteins (OMPs) were analysed by SDS-PAGE and OmpA by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry. Expression of omp and bla genes was analysed by RT-PCR. RESULTS: Isolates EC19 and EC21 had identical PFGE profiles, whereas EC18 was distinct. PCR and IEF confirmed ß-lactamases with pIs of 5.4 (TEM-1) in EC18 and 7.4 (OXA-1) in both EC19 and EC21. EC18 had bla(TEM-1b) with the strong promoter P5 and lacked OmpC and OmpF. RT-PCR showed stronger expression of bla(OXA-1) in EC21 versus EC19, along with diminished expression of OmpC, though with increased OmpF. Plasmids extracted from EC18 and EC21 conferred increased MICs of cefpirome and cefepime, although susceptibility to cefotaxime and ceftazidime was retained. CONCLUSIONS: The 'cefpiromase' or 'cefepimase' ESBL phenotype of the clinical isolates non-susceptible to cefpirome and cefepime resulted from high expression of TEM-1 or OXA-1 ß-lactamases combined with loss of porins.