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.

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, zoophilic 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 <60 year olds, proportion of all fungal positives). Trichophyton rubrum was the most prevalent pathogen detected, accounting for 53% of all dermatophytes detected, 61% of those detected from nail samples and 34% from skin and hair samples. Trichophyton tonsurans was the most prevalent dermatophyte in tinea capitis, accounting for 37% of dermatophytes detected. Both of these organisms are anthropophilic, and this group showed consistently increased prevalence in proportion to all fungal isolates. The proportion of this dermatophyte class (anthropophiles) increased among both nail samples and skin/hair samples during the study period, from 55% of samples in the first 5 years of the study (2001-2005) to 88% (proportion of dermatophytes) in the final 5 years. Conversely, yeast detection decreased. 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.

Determinants and outcomes of access-related blood-stream infections among Irish haemodialysis patients; a cohort study.

BACKGROUND: Infections are the second leading cause of death and hospitalisation among haemodialysis (HD) patients. Rates of access-related bloodstream infections (AR-BSI) are influenced by patient characteristics and local protocols. We explored factors associated with AR-BSI in a contemporary cohort of HD patients at a tertiary nephrology centre. METHODS: A retrospective cohort of 235 chronic HD patients was identified from a regional dialysis programme between Jan 2015 and Dec 2016. Data on demographics, primary renal disease, comorbid conditions and dialysis access type were obtained from the Kidney Disease Clinical Patient Management System (KDCPMS). Data on blood cultures were captured from the microbiology laboratory. Poisson regression with robust variance estimates was used to compare infection rates and relative risk of AR-BSI according to the site and type of vascular access. RESULTS: The mean age was 65 (± 15) years, 77% were men, and the median follow up was 19 months (IQR: 10-24 months), accumulating 2030 catheter-months and 1831 fistula-months. Overall rates of AR-BSI were significantly higher for central venous catheter (CVC) compared to arteriovenous fistula (AVF), (2.22, 95% (CI): 1.62-2.97) versus 0.11 (0.01-0.39) per 100 patient-months respectively), with a rate ratio of 20.29 (4.92-83.66), p < 0.0001. This pattern persisted across age, gender and diabetes subgroups. Within the CVC subgroup, presence of a femoral CVC access was associated with significantly higher rates of AR-BSI (adjusted RR 4.93, 95% CI: 2.69-9.01). Older age (75+ versus < 75 years) was not associated with significant differences in rates of AR-BSI in the unadjusted or the adjusted analysis. Coagulase negative Staphylococcus (61%) and Staphylococcus aureus (23%) were the predominant culprits. AR-BSIs resulted in access loss and hospitalisation in 57 and 72% of events respectively, and two patients died with concurrent AR-BSI. CONCLUSIONS: Rates of AR-BSI are substantially higher in CVC than AVF in contemporary HD despite advances in catheter design and anti-infective protocols. This pattern was consistent in all subgroups. The policy of AVF preference over CVC should continue to minimise patient morbidity while at the same time improving anti-infective strategies through better care protocols and infection surveillance.

Detection of Neisseria meningitidis in a paediatric patient with septic arthritis using multiplexed diagnostic PCR targeting meningitis/encephalitis (ME).

BACKGROUND: Neisseria meningitidis is associated with meningitis and septicemia. Septic meningococcal arthritis is relatively uncommon and its diagnosis associated with clinical and microbiological challenges. Early recognition and treatment is required to prevent joint destruction. PURPOSE: We describe a case of an eleven-year-old boy with septic arthritis and the first reported use of a multiplexed diagnostic PCR test, capable of simultaneous rapid detection of 14 pathogens directly from CSF samples, to determine presence of N. meningitides in a synovial fluid sample. RESULTS: In this case, blood cultures and an aspiration of the joint fluid were negative for microbial growth, but leucocytes were present. Analysis of samples using the multiplexed FilmArray® meningitis/encephalitis panel (MEP) proved positive for N. meningitidis. In parallel, samples forwarded to an accredited reference laboratory confirmed the findings by bacterial 16S rRNA gene amplification and sequencing. Subsequent to these results, empiric treatment with intravenous flucloxacillin was discontinued and oral amoxicillin administered for 1 month. The status of the patient improved with etiology-based antimicrobial therapy. CONCLUSIONS: This case demonstrates difficulties associated with clinical and microbiological diagnosis of primary septic meningococcal arthritis. We describe the first successful use of the FilmArray® MEP assay in detection of N. meningitidis in that context.

Monocarboxylate transporter 1 deficiency and ketone utilization.

Ketoacidosis is a potentially lethal condition caused by the imbalance between hepatic production and extrahepatic utilization of ketone bodies. We performed exome sequencing in a patient with recurrent, severe ketoacidosis and identified a homozygous frameshift mutation in the gene encoding monocarboxylate transporter 1 (SLC16A1, also called MCT1). Genetic analysis in 96 patients suspected of having ketolytic defects yielded seven additional inactivating mutations in MCT1, both homozygous and heterozygous. Mutational status was found to be correlated with ketoacidosis severity, MCT1 protein levels, and transport capacity. Thus, MCT1 deficiency is a novel cause of profound ketoacidosis; the present work suggests that MCT1-mediated ketone-body transport is needed to maintain acid-base balance.

The first occurrence of a CTX-M ESBL-producing Escherichia coli outbreak mediated by mother to neonate transmission in an Irish neonatal intensive care unit.

BACKGROUND: Escherichia coli (E. coli) comprise part of the normal vaginal microflora. Transfer from mother to neonate can occur during delivery resulting, sometimes, in neonatal bacterial disease. Here, we aim to report the first outbreak of CTX-M ESBL-producing E. coli with evidence of mother-to-neonate transmission in an Irish neonatal intensive care unit (NICU) followed by patient-to-patient transmission. METHODS: Investigation including molecular typing was conducted. Infection was defined by clinical and laboratory criteria and requirement for antimicrobial therapy with or without positive blood cultures. Colonisation was determined by isolation without relevant symptoms or indicators of infection. RESULTS: Index case was an 8-day-old baby born at 34 weeks gestation who developed ESBL-producing E. coli infections at multiple body sites. Screening confirmed their mother as colonised with ESBL-producing E. coli. Five other neonates, in the NICU simultaneously with the index case, also tested positive. Of these, four were colonised while one neonate developed sepsis, requiring antimicrobial therapy. The second infected neonate's mother was also colonised by ESBL-producing E. coli. Isolates from all eight positive patients (6 neonates, 2 mothers) were compared using pulsed-field gel electrophoresis (PFGE). Two distinct ESBL-producing strains were implicated, with evidence of transmission between mothers and neonates for both strains. All isolates were confirmed as CTX-M ESBL-producers. There were no deaths associated with the outbreak. CONCLUSIONS: Resources were directed towards control interventions focused on hand hygiene and antimicrobial stewardship, which ultimately proved successful. Since this incident, all neonates admitted to the NICU have been screened for ESBL-producers and expectant mothers are screened at their first antenatal appointment. To date, there have been no further outbreaks.

The first reported case of Burkholderia contaminans in patients with cystic fibrosis in Ireland: from the Sargasso Sea to Irish Children.

BACKGROUND: Burkholderia contaminans is an emerging pathogen in the cystic fibrosis (CF) setting. Included in the Burkholderia cepacia complex (Bcc), B. contaminans is a Gram negative, motile, obligate aerobe previously classified as a pseudomonad. Previous reports have described B. contaminans isolation from patients in Portugal, Switzerland, Spain, Argentina and the USA. This, however, is the first report relating to B. contaminans affecting Irish patients with CF, initially detected in a paediatric setting. CASE PRESENTATION: Burkholderia contaminans was identified in the routine analysis of sputum from a fourteen year old boy, at his annual review and subsequently from the sputum from his 19 year old brother. RecA gene sequencing and pulsed field gel electrophoresis (PFGE) were unable to distinguish between the isolates, which demonstrated with susceptibility to ciprofloxacin, cotrimoxazole, meropenem, pipercillin/tazobactam and ceftazidime. Both isolates were resistant to aztreonam, with reduced susceptibility to tobramycin. Following treatment with intravenous meropenem and ceftazidime, oral ciprofloxacin and nebulised tobramycin for 6 weeks, sputum specimens from both patients were negative for B. contaminans. No other member of the local CF cohort proved positive. CONCLUSIONS: Bcc bacteria are associated with poor prognosis in CF and decreased life expectancy, specifically leading to a more rapid decline in lung function and, in some cases, to a fatal necrotizing pneumonia known as the "cepacia syndrome". Some species exhibit innate resistance to multiple antimicrobial agents and their transmission rate can be high in susceptible patients. In that context, we describe the first incidence of CF-related B. contaminans in Ireland and its successful eradication from two patients, one paediatric, using an aggressive antimicrobial regimen.

A case of failed eradication of cystic fibrosis-related sinus colonisation by Pseudomonas aeruginosa.

BACKGROUND: Pseudomonas aeruginosa is a pathogen associated with cystic fibrosis that has potential to decrease lung function and cause respiratory failure. Paranasal sinuses are increasingly recognised as potential reservoirs for intermittent colonisation by P. aeruginosa. This case documents investigation and outcome of P. aeruginosa recurrence in a male paediatric patient over an eight year period. CASE PRESENTATION: A 12 year old Irish male paediatric cystic fibrosis patient experienced intermittent culturing of P. aeruginosa from the oropharyngeal region, indicating chronic infection of the sinuses despite absence of symptoms, retaining good lung function, and normal bronchoscopy and bronchoalveolar lavage. However, P. aeruginosa was isolated from a sinus wash-out and was identified as a unique strain of P. aeruginosa that was also cultured from cough swabs. Despite treatment, successful eradication from the paranasal sinuses was not achieved. CONCLUSIONS: Few reports have addressed the paranasal sinuses as a reservoir for lung infection in cystic fibrosis patients despite increased recognition of the need to investigate this niche. In this case, attempts at eradication of P. aeruginosa present in paranasal sinuses including oral and nebulised antimicrobials proved unsuccessful. However, detection of P. aeruginosa in the paranasal sinuses instigated antimicrobial treatment which may have contributed to prevention of migration to the lower airways. Our outcome provides additional insight and may indicate utility of nasal lavage or nasal endoscopy in paediatric cystic fibrosis patients' annual review clinic visits.

Seek and you shall find: Yersinia enterocolitica in Ireland's drinking water.

INTRODUCTION: Three Yersinia species were identified from samples of drinking water from diverse geographic regions of Ireland. Conventional commercial biochemical identification systems classified them as Yersinia enterocolitica. Since this organism is the most common cause of bacterial gastroenteritis in some countries, further investigation was warranted. The aim of the study was to provide a microbial characterisation of three Yersinia species, to determine their pathogenicity, and to review the incidence rate of Yersinia enterocolitica detection in our region. METHODS: Organism identification was performed using conventional commercial diagnostic systems MALDI-TOF, API 20E, API 50CHE, TREK Sensititre GNID and Vitek 2 GN, and whole genome sequencing (WGS) was performed. Historical data for detections was extracted from the lab system for 2008 to 2023. RESULTS: All three isolates gave "good" identifications of Yersinia enterocolitica on conventional systems. Further analysis by WGS matched two of the isolates with recently described Yersinia proxima, and the third was a member of the non-pathogenic Yersinia enterocolitica clade 1Aa. DISCUSSION: Our analysis of these three isolates deemed them to be Yersinia species not known currently to be pathogenic, but determining this necessitated the use of next-generation sequencing and advanced bioinformatics. Our work highlights the importance of having this technology available to public laboratories, either locally or in a national reference laboratory. The introduction of molecular technologies for the detection of Yersinia species may increase the rate of detections. Accurate identification of significant pathogens in environmental, public health and clinical microbiology laboratories is critically important for the protection of society.

Neonatal bacteraemia in Ireland: A ten-year single-institution retrospective review.

Neonatal sepsis is a catastrophic condition of global concern, with reported mortality rates exceeding 10%. Bloodstream infections are an important cause of sepsis, and epidemiological studies of these infections are crucial for predicting the most common aetiological agents and antimicrobial susceptibility patterns and for developing antimicrobial guidelines. For the ten-year study period from July 2013 to June 2023, all neonatal bacteraemia cases were reviewed prospectively using an enhanced surveillance protocol. The patients were stratified according to their age at the time of blood culture collection: early onset if diagnosed in the first 72 hours of life, and late onset if diagnosed after that time. During the study period, 170 blood cultures were positive from 144 patients, of which 89 specimens from 64 patients represented the growth of significant pathogens. Coagulase-negative staphylococci (CoNS) were the most common pathogens identified (52%, 33/64), followed by Escherichia coli (14%, 9/64), Group B Streptococcus (GBS: 11%, 7/64) and Staphylococcus aureus (11%, 7/64). GBS was more commonly identified in early onset patients, while CoNS were predominantly associated with late onset. The presence of an intravascular catheter, maternal urinary tract infections and the receipt of total parenteral nutrition or transfused blood were identified as significant risk factors. The fatality rate was 8% (5/64). in summary, this study provides a detailed overview of the epidemiology of neonatal bacteraemia in a large teaching hospital in the Midwest of Ireland over a decade.

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 this study was low but not insignificant and justifies ongoing surveillance of drinking water as a potential source of antimicrobial resistance.

Indwelling central venous catheter infection with Chryseobacterium shandongense - successful eradication in a 5-year-old with cystic fibrosis.

Introduction: Chryseobacterium shandongense is a Gram-negative Flavobacterium bacillus with intrinsic multidrug-resistant properties. Case Presentation: Herein, we present the first case report of human C. shandongense infection, relating to an implantable portal and catheter (port-a-cath) central line in a 5-year-old female with cystic fibrosis. The infection was identified using a Bruker MALDI-TOF Biotyper with BDAL (v12) of blood, which was cultured due to pyrexia and rigour following port-a-cath access. This report details the effective eradication of C. shandongense infection from the port-a-cath device using initial empirical gentamicin followed by targeted ciprofloxacin locks and systemic antibiotics. Conclusion: We demonstrated successful eradication of C. shandongense from a port-a-cath device, including the minimum inhibitory concentrations (MICs) required in this case. The result was eradication of central access infection, preventing progression to bacteraemia/septicaemia and preserving central access in a child with cystic fibrosis and established respiratory disease.

The microbial pathology of maternal perinatal sepsis: A single-institution retrospective five-year review.

INTRODUCTION: Greater than half of in-hospital maternal deaths are caused by sepsis, a condition that occurs when infection exceeds local tissue containment and results in organ dysfunction. Determining the source of infection can be challenging. Microbiological cultures of the uterine cavity are often difficult to obtain, so antimicrobial susceptibility results may not be available to guide treatment. The aim of this retrospective study was to assess the potential clinical value of microbiology samples used in the maternal "septic screen" of patients in an Irish maternity hospital. METHODS: A review was completed of all maternal "septic screen" (i.e., high vaginal swabs, placenta swabs, blood cultures, throat swabs and urine samples) microbiology results from July 2016 to December 2021. RESULTS: In the relevant period, 845 patients were subject to a "septic screen", of whom 430 also had a placental swab collected. These 430 patients comprise our study population. 2% of blood cultures yielded potential pathogens, compared with 37%, 33%, 9% and 7% respectively for placental swabs, high vaginal swabs, throat swabs and urine specimens. 95% of blood cultures were sterile, compared with 52%, 0%, 0% and 53% respectively for placental swabs, high vaginal swabs, throat swabs and urine specimens. CONCLUSION: Of the five microbiological specimen types examined, placental swabs yielded the highest number of potential pathogens. Our results suggest that placental swabs are useful specimens for detecting potential pathogens from the uterine cavity, the most common source of perinatal infections.

Inter-hospital outbreak of Klebsiella pneumoniae producing KPC-2 carbapenemase in Ireland.

OBJECTIVES: To describe an outbreak of KPC-2-producing Klebsiella pneumoniae with inter-hospital spread and measures taken to control transmission. METHODS: Between January and March 2011, 13 K. pneumoniae isolates were collected from nine patients at hospital A and two patients at hospital B. Meropenem, imipenem and ertapenem MICs were determined by Etest, carbapenemase production was confirmed by the modified Hodge method and by a disc synergy test, and confirmed carbapenemase producers were tested for the presence of carbapenemase-encoding genes by PCR. PFGE, plasmid analysis, multilocus variable-number tandem-repeat analysis (MLVA) and multilocus sequence typing (MLST) analysis were performed on all or a subset of isolates. RESULTS: Meropenem, imipenem and ertapenem MICs were 4 to >32, 8-32 and >16 mg/L, respectively. PCR and sequencing confirmed the presence of bla(KPC-2). PFGE identified four distinguishable (≥88%) pulsed-field profiles (PFPs). Isolates distinguishable by PFGE had identical MLVA profiles, and MLST analysis indicated all isolates belonged to the ST258 clone. Stringent infection prevention and control measures were implemented. Over a period of almost 8 months no further carbapenemase-producing Enterobacteriaceae (CPE) were isolated. However, KPC-2-producing K. pneumoniae was detected in two further patients in hospital A in August (PFP indistinguishable from previous isolates) and October 2011 (PFP similar to but distinguishable from previous isolates). CONCLUSIONS: Stringent infection prevention and control measures help contain CPE in the healthcare setting; however, in the case of hospital A, where CPE appears to be established in the population served, it may be virtually impossible to achieve eradication or avoid reintroduction into the hospital.

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.

Outcomes of implementation of the FilmArray meningoencephalitis panel in a tertiary hospital between 2017 and 2020.

BACKGROUND: Acute meningoencephalitis is encountered commonly in the acute hospital setting and is associated with significant morbidity and mortality, in addition to significant healthcare costs. Multiplex PCR panels now allow syndromic testing for central nervous system infection. The BioFire® FilmArray® Meningoencephalitis (ME) allows testing of 14 target pathogens using only 0.2mls of cerebrospinal fluid (CSF). We conducted a retrospective observational study to assess the performance of the assay and secondarily to observe the clinical utility of negative results by comparing clinical outcomes of aseptic meningitis to bacterial and viral meningoencephalitis. METHODS: Data for CSF samples tested using the FilmArray ME panel from October 2017 to October 2020 were analysed. Detection of bacterial and viral targets was analysed. Admission to critical care area, 90-day readmission rates, average length of stay and 30-day and 90-day mortality were analysed for three groups with following diagnoses: bacterial meningitis, viral meningoencephalitis, or aseptic meningitis. RESULTS: From October 2017 to October 2020, 1926 CSF samples were received in the Clinical Microbiology laboratory. Of those, 543 CSF samples from 512 individual patients were tested using the FilmArray ME panel. Twenty-one bacterial targets and 56 viral targets were detected during the study period. For viral targets, the cumulative specificity was 98.9% (95% confidence interval: 93.1-99.9) when compared to the reference laboratory methods. The outcomes for 30- and 90-day mortality of the aseptic meningitis group were non-inferior relative to the viral meningoencephalitis and bacterial meningitis group. Patients with bacterial meningitis had a longer average length of stay. Aseptic meningitis was associated with a higher 90-day readmission rate than the other 2 groups, but without statistical significance. CONCLUSION: In our hands, implementation of the FilmArray ME panel was relatively straightforward. We experienced a transition in our workflow processes that enabled streamlining of CSF diagnostics and the safe removal of Gram staining in those samples being tested by this molecular assay. Coupled to this improvement, there was a positive clinical impact on patient care due to rapid turnaround time to results.

Osteosynthesis-associated infection of the lower limbs by multidrug-resistant and extensively drug-resistant Gram-negative bacteria: a multicentre cohort study.

Purpose: The purpose of this study was the clinical and therapeutic assessment of lower-limb osteosynthesis-associated infection (OAI) by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Gram-negative bacteria (GNB), which have been poorly studied to date. Methods: A prospective multicentre observational study was conducted on behalf of ESGIAI (the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group on Implant-Associated Infections). Factors associated with remission of the infection were evaluated by multivariate and Cox regression analysis for a 24-month follow-up period. Results: Patients ( n = 57 ) had a history of trauma (87.7 %), tumour resection (7 %) and other bone lesions (5.3 %). Pathogens included Escherichia coli ( n = 16 ), Pseudomonas aeruginosa ( n = 14 ; XDR 50 %), Klebsiella spp. ( n = 7 ), Enterobacter spp. ( n = 9 ), Acinetobacter spp. ( n = 5 ), Proteus mirabilis ( n = 3 ), Serratia marcescens ( n = 2 ) and Stenotrophomonas maltophilia ( n = 1 ). The prevalence of ESBL (extended-spectrum ß -lactamase), fluoroquinolone and carbapenem resistance were 71.9 %, 59.6 % and 17.5 % respectively. Most patients ( n = 37 ; 64.9 %) were treated with a combination including carbapenems ( n = 32 ) and colistin ( n = 11 ) for a mean of 63.3 d. Implant retention with debridement occurred in early OAI (66.7 %), whereas the infected device was removed in late OAI (70.4 %) ( p = 0.008 ). OAI remission was achieved in 29 cases (50.9 %). The type of surgery, antimicrobial resistance and duration of treatment did not significantly influence the outcome. Independent predictors of the failure to eradicate OAI were age > 60  years (hazard ratio, HR, of 3.875; 95 % confidence interval, CI95 %, of 1.540-9.752; p = 0.004 ) and multiple surgeries for OAI (HR of 2.822; CI95 % of 1.144-6.963; p = 0.024 ). Conclusions: Only half of the MDR/XDR GNB OAI cases treated by antimicrobials and surgery had a successful outcome. Advanced age and multiple surgeries hampered the eradication of OAI. Optimal therapeutic options remain a challenge.

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

BACKGROUND: 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. CONCLUSION: There was limited impact of 16s PCR results on antimicrobial treatments. Relevance to practice was affected by relatively long turn-around-time for results. Utility may be increased in specialised surgical centres, or by reducing turn-around-time. Enrichment culture should be considered on samples where 16s PCR is requested. There remains limited evidence for use of 18s PCR in clinical management, and further studies in this area are likely warranted.

SARS-CoV-2 infection in general practice in Ireland: a seroprevalence study.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody testing in community settings may help us better understand the immune response to this virus and, therefore, help guide public health efforts. AIM: To conduct a seroprevalence study of immunoglobulin G (IgG) antibodies in Irish GP clinics. DESIGN & SETTING: Participants were 172 staff and 799 patients from 15 general practices in the Midwest region of Ireland. METHOD: This seroprevalence study utilised two manufacturers' point-of-care (POC) SARS-CoV-2 immunoglobulin M (IgM)-IgG combined antibody tests, which were offered to patients and staff in general practice from 15 June to 10 July 2020. RESULTS: IgG seroprevalence was 12.6% in patients attending general practice and 11.1% in staff working in general practice, with administrative staff having the lowest seroprevalence at 2.5% and nursing staff having the highest at 17.6%. Previous symptoms suggestive of COVID-19 and history of a polymerase chain reaction (PCR) test were associated with higher seroprevalence. IgG antibodies were detected in approximately 80% of participants who had a previous PCR-confirmed infection. Average length of time between participants' positive PCR test and positive IgG antibody test was 83 days. CONCLUSION: Patients and healthcare staff in general practice in Ireland had relatively high rates of IgG to SARS-CoV-2 compared with the national average between 15 June and 10 July 2020 (1.7%). Four-fifths of participants with a history of confirmed COVID-19 disease still had detectable antibodies an average of 12 weeks post-infection. While not proof of immunity, SARS-CoV-2 POC testing can be used to estimate IgG seroprevalence in general practice settings.