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千葉大学大学院人文社会科学研究科研究プロジェクト報告書第257集『都市コミュニティにおける相互扶助と次世代育成』水島治郎 編Sustainable Urban Communities: Communality and Generativity Report on the Research Projects No.25

A retrospective observational study of the impact of 16s and 18s ribosomal RNA PCR on antimicrobial treatment over seven years: A tertiary hospital experience

Although culture-based methods remain a staple element of microbiology analysis advanced molecular methods increasingly supplement the testing repertoire. Since the advent of 16s and 18s ribosomal RNA PCR in the 2000s, there has been interest in its utility for pathogen detection. Nonetheless, studies assessing the impact on antimicrobial prescribing are limited. We report a single-centre experience of the influence of 16s and 18s PCR testing on antimicrobial treatment, including a cost-analysis. Methods Data were collected retrospectively for all samples sent for 16s and 18s PCR testing between January 2014 and December 2020. Results were compared to any culture-based result. Assessment focused on any change of antimicrobial treatment based on PCR result, or use of the result as supportive evidence for microbiological diagnosis. Results 310 samples relevant to 268 patients were referred for 16s/18s rRNA PCR testing during the period. Culture was performed for 234 samples. Enrichment culture was performed for 83 samples. 82 of 300 samples sent for 16s PCR had positive results (20.8%). When culture was performed, enrichment reduced the outcome of 16s PCR only positive results (4/36 [11.1%] versus 14/35 [40.0%], p = 0.030 where a pathogen found). 18s PCR yielded 9 positive results from 67 samples. The 16s PCR result influenced antimicrobial change for 6 patients (2.2%). We estimated the cost for 16s PCR testing to result in one significant change in antimicrobial therapy to be €3,340. 18s PCR did not alter antimicrobial treatment

Against the onslaught of endemic KPC, the war is being lost on the Irish Front.

In the context of the excellent report of successful control of an outbreak of carbapenemase-producing Klebsiella pneumoniae in an Italian neonatal intensive care unit published in this journal (1), we wish to report the consequences of the first outbreak of KPC-producing Kliebsiella in Ireland and how, despite identification of operational factors associated with the incidence and best efforts towards rectifying those, our 410-bed hospital in the West of Ireland is failing to control endemic KPCs. Globally, there is recognition of the significant morbidity and mortality implications associated with emergence of carbapenemase-producing bacteria (2). The resulting vigilance has resulted in enhanced reporting of outbreaks, many being the first of their kind in specific countries (3), and descriptions of molecular studies to determine incidence and transfer of the carbapenemase-encoding blaKPC-harboring IncFIA plasmid between clonal variants (4). With indicative rates of carriage being circa 20%, infection control specialists are reacting with novel techniques for microbiological detection, strategies for prevention of nosocomial transmission, and clinical microbiologists are facing therapeutic challenges related to limited, relatively unproven antimicrobial treatment options

Antimicrobial resistance Is prevalent in E. coli and other enterobacterales isolated from public and private drinking water supplies in the Republic of Ireland

High levels of bacterial antimicrobial resistance (AMR) have been reported in many environmental studies conducted in Ireland and elsewhere. The inappropriate use of antibiotics in both human and animal healthcare as well as concentrations of residual antibiotics being released into the environment from wastewaters are thought to be contributing factors. Few reports of AMR in drinking water-associated microbes are available for Ireland or internationally. We analysed 201 enterobacterales from group water schemes and public and private water supplies, only the latter having been surveyed in Ireland previously. The organisms were identified using conventional or molecular techniques. Antimicrobial susceptibility testing for a range of antibiotics was performed using the ARIS 2X interpreted in accordance with EUCAST guidelines. A total of 53 Escherichia coli isolates, 37 Serratia species, 32 Enterobacter species and enterobacterales from seven other genera were identified. A total of 55% of isolates were amoxicillin resistant, and 22% were amoxicillin-clavulanic acid resistant. A lower level of resistance (<10%) was observed to aztreonam, chloramphenicol, ciprofloxacin, gentamicin, ceftriaxone and trimethoprim-sulfamethoxazole. No resistance to amikacin, piperacillin/tazobactam, ertapenem or meropenem was detected. The level of AMR detected in thisstudy was low but not insignificant and justifies ongoing surveillance of drinking water as a potential source of antimicrobial resistance.</p

Dermatology mycology diagnostics in Ireland: National deficits identified in 2022 that are relevant internationally

Background: Conventional testing methods for dermatophytes are time-consuming, and resource limitations in our institution have prompted curtailed access to these diagnostics.Objectives: Evaluation of our hospital's dermatological mycology diagnostic services and similar services nationally.Methods: This was a retrospective observational study on skin, hair and nail mycology samples in our institution comparing twenty five-year periods (2011–2015 and 2016–2021), including analysis of dermatology clinic data and correspondence related to fungal infection. A survey of national public hospitals' laboratories was conducted to evaluate their mycology testing capabilities.Results: The total 5 year test count prior to curtailment was 4851 specimens comprising 90% (n = 4344) from general practice and 6% (n = 290) from dermatology clinics. For the 5 years post curtailment, 64.5% (582/903) of specimens were from dermatology clinics. Dermatology clinic data demonstrated doubling of attendances (for all conditions) and of correspondence related to fungal infection. During this time also, national dermatological antifungal purchasing increased 11%. Ten of 28 Irish public hospital laboratories reported the provision of in-house dermatological mycology testing, and none had routine availability of susceptibility or molecular testing of dermatophytes.Conclusion: This study is the first to report an appraisal of dermatological fungal diagnostic services in Ireland. Insufficient testing capacity implies that patients are either being treated for fungal infection without appropriate diagnostic confirmation, or being left untreated because of the lack of access to diagnostics. The introduction of molecular detection methods and susceptibility systems would enhance testing capabilities and reduce the requirement for the external referral.</p

Epidemiology of dermatomycoses and onychomycoses in Ireland (2001–2020): A single-institution review

Background: Fungal skin infections are recognised as one of the most common health disorders globally, and dermatophyte infections of the skin, hair and nails are the most common fungal infections. Dermatophytes can be classified as anthropophilic, zoo-philic or geophilic species based on their primary habitat association, and this classification makes epidemiological analysis useful for the prevention and control of these infections. The Irish contribution to the epidemiology of these infections has been scant, with just two papers (both reporting paediatric tinea capitis only) published in the last 20 years, and none in the last seven. Objectives: To perform a comprehensive retrospective epidemiological analysis of all dermatological mycology tests performed in University Hospital Limerick over a 20-year period. Methods: All mycology laboratory test results were extracted from the Laboratory Information Management System (LIMS, iLab, DXC Technologies) from 2001 to 2020 inclusive for analysis. Specimen types were categorised according to the site of sampling. The data were analysed using Microsoft Excel. Results: About 12,951 specimens of skin, hair and nails were studied. Median patient age was 42 years (IQR 26–57) with a slight female preponderance (57.2%). Two thirds of samples (67%, n = 8633) were nail, 32% were skin scrapings (n = 4118) and 200 hair samples (1.5%) were received. Zoophilic dermatophytes were more commonly present in females (38% F, 23% M, proportion of dermatophytes) and in those under 10 years of age or from 45 to 70 years (36% and 34% zoophiles, respectively, proportion of dermatophytes), although anthropophiles predominated every age and gender category. Anthropophiles had their highest prevalence in the 10–20 years age category (80% anthropophiles, proportion of dermatophytes), and yeast infections were more prevalent in older patients (29% of >60 year olds vs. 17% of Conclusions: This study provides a detailed overview of the epidemiology of the fungal cultures of skin, nail and hair samples in the Mid-West of Ireland over a 20-year period. Monitoring this changing landscape is important in identifying likely sources of infections, to identifying potential outbreaks, and may help guide empiric treatment. To the best of our knowledge, this study provides the first detailed analysis from Ireland of fungal detections from skin, hair and nail samples, and is the first epidemiological fungal report of any kind in over 7 years. </p

Prevalence of linezolid‑resistant organisms among patients admitted to a tertiary hospital for critical care or dialysis

Background Linezolid is an oxazolidinone antimicrobial regarded as a “last resort” antimicrobial, used typically for treatment of Gram-positive bacterial infections. It is acknowledged that prevalence of resistance to linezolid is increasing in Europe. In Ireland, a number of outbreaks of linezolid-resistant isolates have been reported, including an outbreak at the location for this study, the Intensive Care Unit (ICU) of University Hospital Limerick (UHL). Methods The Chromagar™ Lin-R selective medium was validated using a panel of linezolid-sensitive and linezolid-resistant strains. Subsequently, the prevalence exercise focused on a convenience sample of patients (n=159) in critical care wards, ICU (n=23) and High-Dependency Unit (HDU, n=51), in addition to patients undergoing dialysis therapy (n=77). Eight additional patients had specimens collected when attending more than one location. Growth on Chromagar™ Lin-R agar was followed by drug sensitivity testing by disc diffusion and minimum inhibitory concentration (MIC) testing. Results A validation exercise was performed on 23 isolates: seven target and sixteen non-target organisms. Isolates performed as intended (100% sensitivity, 100% specificity). For the prevalence study, of 398 tests, 40 resulted in growth of non-target organisms (specificity approx. 90%). A sole patient (1/159) was identified as colonized by a linezolid-resistant Staphylococcus epidermidis, a prevalence of 0.63%. Molecular investigation confirmed presence of the G2576T mutation in the 23S rRNA. Conclusion While this point prevalence study identified extremely low carriage of linezolid-resistant bacteria, it remains prudent to maintain vigilance as reports of outbreaks associated with linezolid-resistant S. epidermidis (LRSE) in European critical care units are increasing

Colonisation with extended-spectrum beta-lactamase (ESBL) not detected in a prevalence study.

Background The Mid-West of Ireland has higher than average national rates of invasive extended-spectrum beta-lactamase (ESBL) bloodstream infections and carbapenemase-producing Enterobacteriaceae (CPE), with increasing numbers of ESBL isolates detected in community-dwelling patients. Aims To conduct a point prevalence study in a convenience sample of the Mid-West population with the aim of determining the extent of ESBL colonisation Methods Utilising anonymised community stool samples that had completed routine analysis, we conducted a point prevalence study over a four-week period on all samples that met defined inclusion and exclusion criteria. Limited epidemiological data was recorded: (1) age of patient, (2) gender, (3) sender location. From these stool specimens, rectal swabs were inoculated (eSwab™ 480CE, Copan, Italy), which were subsequently cultured on selective chromogenic agar (Colorex™ ESBL). Culture plates were incubated aerobically at 37˚C for 24 hours. Results Of 195 samples processed, 58% (n=112) were from females. The median patient age was 62.4 years (range 20-94 years). 186 samples (95%) originated from general practitioner clinics. During the study period, only nine eligible stool samples were received from LTCF (6 public). From 195 Colorex™ ESBL chromogenic agar plates cultured, no ESBL-producing organisms were detected. Conclusions This community point prevalence study did not identify ESBL-colonisation despite high numbers of patients with invasive ESBL bloodstream infections presenting for admission in our institution. We believe this may be because of our small sample size. Data regarding antimicrobial exposure and other risk factors for ESBL-colonisation was also not available. We remain vigilant for ESBL-producing organisms

Additional file 1: Figure S1. of Serum and synovial fluid cytokine profiling in hip osteoarthritis: distinct from knee osteoarthritis and correlated with pain

Presence of MDC, IL6 and IP10 in Hip OA, Knee OA and control synovium, synovial fluid and serum not corrected for multiple comparisons. Table S1. Biochemical markers that have been reported to be correlated with OA pain. Table S2. Questionnaire scores of hip OA cohort. Table S3. Correlations between cytokine concentrations and hip pain. (DOCX 140 kb

Candidaemia in an Irish intensive care unit setting between 2004 and 2018 reflects increased incidence of Candida glabrata

The cumulative incidence of candidaemia in an Irish intensive care unit (ICU) setting between January 2004 and August 2018 was 17/1000 ICU admissions. Candida albicans was responsible for 55% (N=41) of cases. C. glabrata (N=21, 28%) was the next most prevalent species, and has been identified most frequently since 2012. C. glabrata was associated with a higher mortality rate (57%) than C. albicans (29%). All isolates were susceptible to caspofungin (0.05 μg/mL). Notably, 37% of C. glabrata isolates were resistant to fluconazole, with 13% resistant to amphotericin B, highlighting the need for prudent antifungal stewardship to impede development of multi-drug-resistant C. glabrata in the ICU setting