Increase in Community Acquired S. aureus Bloodstream Infection Associated with the Sars-Cov-2 Public Health Emergency.

Aim In March 2020, a public health emergency related to COVID-19 was declared in Ireland, resulting in certain healthcare restrictions. We hypothesised, in the microbiology laboratory in Galway University Hospital (GUH), that the national lockdown would impact results from our blood culture service. Methods A surveillance review of all blood cultures received in the microbiology laboratory in GUH for the six-month period March-August 2020 was performed and compared to the same time-period for the preceding four years. Patient demographics and blood culture isolates were collected and reviewed. Results From March to August 2020, 5,753 blood culture sets were tested, of which 6.1% (n=351) were positive; a lower positivity rate than in previous years. In 2020, 46 S. aureus isolates were detected in blood cultures (representing 13.1% of all 351 positive blood cultures), which was significantly higher than 2016-2019. Conclusion The higher number of reported S. aureus bloodstream infections in the SARS-CoV-2-era was unexpected.

Spontaneous Escherichia coli Meningitis and Pyogenic Ventriculitis in an Adult Receiving Anti-Tumour Necrosis Factor Alpha Therapy.

Presentation A 60-year-old male taking etanercept for ankylosing spondylitis was admitted to hospital with confusion and reduced level of consciousness over the preceding 24 hours. Diagnosis Magnetic Resonance Imaging (MRI) of his brain revealed pyogenic ventriculitis, and Escherichia coli was cultured from CSF. Treatment He required placement of an external ventricular drain and was treated with a prolonged course of intravenous ceftriaxone. Conclusion To our knowledge, this is the first reported case of spontaneous Gram-negative bacillary meningitis in a patient on anti-tumour necrosis factor (TNF)-alpha therapy, highlighting the risk of rare but serious infections associated with this class of medication.

Investigation of a foodborne outbreak of Shigella sonnei in Ireland and Northern Ireland, December 2016: the benefits of cross-border collaboration and commercial sales data.

OBJECTIVES: To describe a cross-border foodborne outbreak of Shigella sonnei that occurred in Ireland and Northern Ireland (NI) in December 2016 whilst also highlighting the valuable roles of sales data and international collaboration in the investigation and control of this outbreak. STUDY DESIGN: A cross-border outbreak control team was established to investigate the outbreak. METHODS: Epidemiological, microbiological, and environmental investigations were undertaken. Traditional analytical epidemiological studies were not feasible in this investigation. The restaurant chain provided sales data, which allowed assessment of a possible increased risk of illness associated with exposure to a particular type of heated food product (product A). RESULTS: Confirmed cases demonstrated sole trimethoprim resistance: an atypical antibiogram for Shigella isolates in Ireland. Early communication and the sharing of information within the outbreak control team facilitated the early detection of the international dimension of this outbreak. A joint international alert using the European Centre for Disease Control's confidential Epidemic Intelligence Information System for Food- and Waterborne Diseases and Zoonoses (EPIS-FWD) did not reveal further cases outside of the island of Ireland. The outbreak investigation identified that nine of thirteen primary case individuals had consumed product A from one of multiple branches of a restaurant chain located throughout the island of Ireland. Product A was made specifically for this chain in a food production facility in NI. S. sonnei was not detected in food samples from the food production facility. Strong statistical associations were observed between visiting a branch of this restaurant chain between 5 and 9 December 2016 and eating product A and developing shigellosis. CONCLUSIONS: This outbreak investigation highlights the importance of international collaboration in the efficient identification of cross-border foodborne outbreaks and the value of using sales data as the analytical component of such studies.

Antimicrobial prescribing and infections in long-term care facilities (LTCF): a multilevel analysis of the HALT 2016 study, Ireland, 2017.

BackgroundThe 2016 point prevalence survey (PPS) of healthcare-associated infections (HAI) and antimicrobial use (AMU) in Irish long-term care facilities (LTCF) (HALT) showed a 9.8% AMU and 4.4% HAI prevalence, based on aggregated data analysis.AimOur aim was to identify institutional and resident risk factors of AMU and HAI.MethodsHALT 2016 gathered information using institutional and resident questionnaires, for residents who met the surveillance definition of active HAI and/or AMU, limiting analysis to the aggregated institutional level. In January 2017, we requested additional data on age, sex, urinary catheter use and disorientation of current residents from HALT 2016 LTCF and matched to 2016 HALT data.ResultsOf 224 HALT 2016 LTCF, 80 provided additional information on 3,816 residents; prevalence of AMU was 10.6% and HAI was 4.7%. Presence of a coordinating physician (Odds ratio (OR): 0.3; 95% confidence interval (CI): 0.2-0.6), antimicrobial stewardship committee (OR: 0.2; 95%; CI: 0.1-0.6), healthcare assistants (OR: 0.9; 95% CI: 0.9-1.0), antimicrobial consumption feedback (OR: 0.3; 95% CI: 0.1-0.6) and medical care by personal general practitioner (OR: 0.6; 95% CI: 0.7-1.0) were associated with less AMU and feedback on surveillance of infection prevention and control (IPC) practices (OR: 0.6; 95% CI: 0.3-1.0) with less HAI. AMU and HAI varied significantly between LTCF.ConclusionsMultilevel modelling identified significant inter-facility variation, as well as institutional factors associated with AMU and HAI. An antimicrobial stewardship committee linked with feedback on IPC and prescribing was associated with reduced AMU and HAI.

Antimicrobial compounds (triclosan and triclocarban) in sewage sludges, and their presence in runoff following land application.

The reuse of treated municipal sewage ('biosolids') on land is an effective method to divert waste away from landfill and to use an alternative, low cost method of fertilisation. While legislation has mainly focused on the control of nutrient and metal application rates to land, other potentially harmful emerging contaminants (ECs) may be present in biosolids. Up to 80% of municipal sewage sludge is reused in agriculture in Ireland, which is currently the highest rate of reuse in Europe. However, unlike other countries, no study has been conducted on the presence of ECs across a range of wastewater treatment plants (WWTPs) in this country. This study evaluated the concentrations of two ECs in sewage sludge, the antimicrobials triclosan (TCS) and triclocarban (TCC), and their presence in surface runoff following land application in controlled rainfall simulation studies. In 16 WWTPs, concentrations of TCS and TCC were 0.61 and 0.08µgg-1, which is at the lower end of concentrations measured in other countries. The concentrations in runoff post land application were also mainly below the limits of detection (90ngL-1 for TCS, 6ngL-1 for TCC), indicating that runoff is not a significant pathway of entry into the environment.

Antimicrobial-resistant Faecal Organisms in Algae Products Marketed as Health Supplements.

Dietary supplements are increasingly popular in Irish society. One of these is blue-green algae which is used with a variety health benefits in mind. A batch of Chlorella powder was found to be contaminated with Salmonella species in Ireland in 2015. This prompted additional testing of a total of 8 samples of three different products (Chlorella, Spirulina and Super Greens), for other faecal flora and antimicrobial resistance in any bacteria isolated. All 8 samples cultured enteric flora such as Enterococci, Enterobacteriaceae and Clostridium species. Antimicrobial susceptibility testing revealed one isolate with extended-spectrum ?-lactamase (ESBL) activity and one with carbapenemase activity. Clinicians caring for vulnerable patients should be aware of the potential risk of exposure to antimicrobial resistant bacteria associated with these products.

Whole genome sequencing provides insights into the genetic determinants of invasiveness in Salmonella Dublin.

Salmonella enterica subsp. enterica serovar Dublin (S. Dublin) is one of the non-typhoidal Salmonella (NTS); however, a relatively high proportion of human infections are associated with invasive disease. We applied whole genome sequencing to representative invasive and non-invasive clinical isolates of S. Dublin to determine the genomic variations among them and to investigate the underlying genetic determinants associated with invasiveness in S. Dublin. Although no particular genomic variation was found to differentiate in invasive and non-invasive isolates four virulence factors were detected within the genome of all isolates including two different type VI secretion systems (T6SS) encoded on two Salmonella pathogenicity islands (SPI), including SPI-6 (T6SSSPI-6) and SPI-19 (T6SSSPI-19), an intact lambdoid prophage (Gifsy-2-like prophage) that contributes significantly to the virulence and pathogenesis of Salmonella serotypes in addition to a virulence plasmid. These four virulence factors may all contribute to the potential of S. Dublin to cause invasive disease in humans.

Whole genome sequencing provides an unambiguous link between Salmonella Dublin outbreak strain and a historical isolate.

Salmonella enterica subsp. enterica serovar Dublin is an uncommon cause of human salmonellosis; however, a relatively high proportion of cases are associated with invasive disease. The serotype is associated with cattle. A geographically diffuse outbreak of S. Dublin involving nine patients occurred in Ireland in 2013. The source of infection was not identified. Typing of outbreak associated isolates by pulsed-field gel electrophoresis (PFGE) was of limited value because PFGE has limited discriminatory power for S. Dublin. Whole genome sequencing (WGS) showed conclusively that the isolates were closely related to each other, to an apparently unrelated isolate from 2011 and distinct from other isolates that were not readily distinguishable by PFGE.

Dissemination of clonally related multidrug-resistant Klebsiella pneumoniae in Ireland.

In October 2012, an outbreak of gentamicin-resistant, ciprofloxacin non-susceptible extended-spectrum ß-lactamase (ESBL)-producing Klebsiella pneumoniae occurred in a neonatal intensive care unit in Ireland. In order to determine whether the outbreak strain was more widely dispersed in the country, 137 isolates of K. pneumoniae with this resistance phenotype collected from 17 hospitals throughout Ireland between January 2011 and July 2013 were examined. ESBL production was confirmed phenotypically and all isolates were screened for susceptibility to 19 antimicrobial agents and for the presence of genes encoding bla TEM, bla SHV, bla OXA, and bla CTX-M; 22 isolates were also screened for bla KPC, bla NDM, bla VIM, bla IMP and bla OXA-48 genes. All isolates harboured bla SHV and bla CTX-M and were resistant to ciprofloxacin, gentamicin, nalidixic acid, amoxicillin-clavulanate, and cefpodoxime; 15 were resistant to ertapenem, seven to meropenem and five isolates were confirmed as carbapenemase producers. Pulsed-field gel electrophoresis of all isolates identified 16 major clusters, with two clusters comprising 61% of the entire collection. Multilocus sequence typing of a subset of these isolates identified a novel type, ST1236, a single locus variant of ST48. Data suggest that two major clonal groups, ST1236/ST48 (CG43) and ST15/ST14 (CG15) have been circulating in Ireland since at least January 2011.

Characterization of methicillin-resistant Staphylococcus aureus from residents and the environment in a long-term care facility.

Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health concern associated with residence in a long-term care facility (LTCF). The aim of this prospective study was to characterize MRSA isolated from residents over a 1-year period and their physical environment over a 2-year period. MRSA was recovered from 17/64 residents (R) of a LTCF and from 42 environmental (E) sites. All isolates carried the mecA gene and lacked the mecC and Panton-Valentine leukocidin (PVL) genes. Thirteen spa types were identified with t032 being the most frequent (41% of total; n = 8R, 16E), followed by t727 (22% of total; n = 13E), and t8783 (10% of total; n = 6E). Five spa types were each represented by single isolates. Thirty-nine isolates were of spa types associated with the multilocus sequence type ST22 (t032, 41%; spa-CC22, 68%) and reflect the predominance of ST22 in Irish hospitals. The uncommon spa types t727, t8783, t1372, t3130, t10038 were present in the environment but not detected in residents and are infrequently observed in Ireland.

Commonly used disinfectants fail to eradicate Salmonella enterica biofilms from food contact surface materials.

Salmonellosis is the second most common cause of food-borne illness worldwide. Contamination of surfaces in food processing environments may result in biofilm formation with a risk of food contamination. Effective decontamination of biofilm-contaminated surfaces is challenging. Using the CDC biofilm reactor, the activities of sodium hypochlorite, sodium hydroxide, and benzalkonium chloride were examined against an early (48-h) and relatively mature (168-h) Salmonella biofilm. All 3 agents result in reduction in viable counts of Salmonella; however, only sodium hydroxide resulted in eradication of the early biofilm. None of the agents achieved eradication of mature biofilm, even at the 90-min contact time. Studies of activity of chemical disinfection against biofilm should include assessment of activity against mature biofilm. The difficulty of eradication of established Salmonella biofilm serves to emphasize the priority of preventing access of Salmonella to postcook areas of food production facilities.

International outbreak investigation of Salmonella Heidelberg associated with in-flight catering.

Rapid and wide dispersal of passengers after flights makes investigation of flight-related outbreaks challenging. An outbreak of Salmonella Heidelberg was identified in a group of Irish travellers returning from Tanzania. Additional international cases sharing the same flight were identified. Our aim was to determine the source and potential vehicles of infection. Case-finding utilized information exchange using experts' communication networks and national surveillance systems. Demographic, clinical and food history information was collected. Twenty-five additional cases were identified from Ireland, The Netherlands, Norway, USA and Canada. We conducted a case-control study which indicated a significant association between illness and consumption of milk tart (OR 10.2) and an egg dish (OR 6) served on-board the flight. No food consumed before the flight was associated with illness. Cases from countries other than Ireland provided supplementary information that facilitated the identification of likely vehicles of infection. Timely, committed international collaboration is vital in such investigations.

A multi-country outbreak of Salmonella Newport gastroenteritis in Europe associated with watermelon from Brazil, confirmed by whole genome sequencing: October 2011 to January 2012.

In November 2011, the presence of Salmonella Newport in a ready-to-eat watermelon slice was confirmed as part of a local food survey in England. In late December 2011, cases of S. Newport were reported in England, Wales, Northern Ireland, Scotland, Ireland and Germany. During the outbreak, 63 confirmed cases of S. Newport were reported across all six countries with isolates indistinguishable by pulsed-field gel electrophoresis from the watermelon isolate.A subset of outbreak isolates were whole-genome sequenced and were identical to, or one single nucleotide polymorphism different from the watermelon isolate.In total, 46 confirmed cases were interviewed of which 27 reported watermelon consumption. Further investigations confirmed the outbreak was linked to the consumption of watermelon imported from Brazil.Although numerous Salmonella outbreaks associated with melons have been reported in the United States and elsewhere, this is the first of its kind in Europe.Expansion of the melon import market from Brazil represents a potential threat for future outbreaks. Whole genome sequencing is rapidly becoming more accessible and can provide a compelling level of evidence of linkage between human cases and sources of infection,to support public health interventions in global food markets.

Investigation and management of an outbreak of Salmonella Typhimurium DT8 associated with duck eggs, Ireland 2009 to 2011.

Salmonella Typhimurium DT8 was a very rare cause of human illness in Ireland between 2000 and 2008, with only four human isolates from three patients being identified. Over a 19-month period between August 2009 and February 2011, 34 confirmed cases and one probable case of Salmonella Typhimurium DT8 were detected, all of which had an MLVA pattern 2-10-NA-12-212 or a closely related pattern. The epidemiological investigations strongly supported a linkbetween illness and exposure to duck eggs. Moreover, S. Typhimurium with an MLVA pattern indistinguishable (or closely related) to the isolates from human cases, was identified in 22 commercial and backyard duck flocks, twelve of which were linked with known human cases. A range of control measures were taken at farm level, and advice was provided to consumers on the hygienic handling and cooking of duck eggs. Although no definitive link was established with a concurrent duck egg-related outbreak of S. Typhimurium DT8 in the United Kingdom, it seems likely that the two events were related. It may be appropriate for other countries with a tradition of consuming duck eggs to consider the need for measures to reduce the risk of similar outbreaks.

Isolation of NDM-1-producing Klebsiella pnemoniae in Ireland, July 2011.

We report the identification of New Delhi metallo-betalactamase 1 (NDM-1)-producing Klebsiella pnemoniae in Ireland. The organism was resistant to multiple antibiotic classes, including carbapenems, and PCR and sequencing confirmed the presence of the blaNDM-1 gene, carried on a 98 kb plasmid. The organism was isolated from an infant, who was born in India and moved to Ireland at the age of four months. This is the first reported isolation of an NDM-1-producing Enterobacteriaceae strain in Ireland.

Salmonella enterica serovar Agona European outbreak associated with a food company.

We investigated an international outbreak of Salmonella Agona with a distinct PFGE pattern associated with an Irish Food company (company X) producing pre-cooked meat products sold in various food outlet chains in Europe. The outbreak was first detected in Ireland. We undertook national and international case-finding, food traceback and microbiological investigation of human, food and environmental samples. We undertook a matched case-control study on Irish cases. In total, 163 cases in seven European countries were laboratory-confirmed. Consumption of food from food outlet chains supplied by company X was significantly associated with being a confirmed case (mOR 18·3, 95% CI 2·2-149·2) in the case-control study. The outbreak strain was isolated from the company's pre-cooked meat products and production premises. Sufficient evidence was gathered to infer the vehicles of infection and sources of the outbreak and to justify the control measures taken, which were plant closure and food recall.

Restoring the selectivity of Bolton broth during enrichment for Campylobacter spp. from raw chicken.

AIMS: When isolating Campylobacter spp. from retail raw chicken using BS EN ISO 10272-1:2006, contaminants frequently cause overgrowth on mCCDA plates. Therefore, these organisms proliferate in the enrichment medium, Bolton broth, indicating a lack of selectivity in this medium. This study sought to characterize the contaminant flora and to devise a modified Bolton broth to inhibit their growth. METHODS AND RESULTS: Contaminants (n=30) from separate samples were identified and antibiotic resistances determined. Most (93%) were extended spectrum ß-lactamase (ESBL) producing Escherichia coli, able to hydrolyse the cefoperazone present in Bolton broth and mCCDA. To inhibit these organisms, original formulation Bolton broth was supplemented with potassium clavulanate, at three concentrations, and recoveries of campylobacters from raw chicken were determined. Using standard Bolton broth, only 49% of samples (n=104) yielded campylobacters, but supplementation with 2 mg l(-1) potassium clavulanate increased this significantly (P<0.05), with 91% of samples positive. CONCLUSIONS: Potassium clavulanate can restore the selectivity of Bolton broth when isolating Campylobacter spp. from raw chicken. SIGNIFICANCE AND IMPACT OF THE STUDY: Raw chicken is often contaminated with the pathogen Campylobacter, but the ISO methodology for its detection is becoming compromised by the increasing presence of antibiotic-resistant bacteria. A simple modification ensures effective detection of this pathogen.

Application of multiple locus variable number of tandem repeat analysis (MLVA), phage typing and antimicrobial susceptibility testing to subtype Salmonella enterica serovar Typhimurium isolated from pig farms, pork slaughterhouses and meat producing plants in Ireland.

Salmonella enterica subsp. enterica serovar Typhimurium is a common zoonotic pathogen encountered in Irish pigs and the pork industry and its characterisation using highly discriminatory typing methods is necessary for epidemiological studies, outbreak investigation and control. Multiple locus variable number of tandem repeat analysis (MLVA), phage typing and antimicrobial susceptibility testing were applied to characterise 301 S. typhimurium isolates of porcine origin isolated from farms, slaughterhouses and pork meat producing plants in Ireland over a four-year period. 154 MLVA patterns were obtained compared to 19 phage types and 38 AMR patterns, and MLVA was particularly useful for discriminating isolates of the same phage type, e.g. DT104 and DT104b, or isolates that were Untypable or in the category of "react with phage but does not conform to a recognised phage type" (RDNC) by the phage typing method. Cluster analysis of MLVA profiles using a minimum spanning tree (MST) demonstrated two major clusters (I and II), which showed to have a clear association with phage types, cluster I associated to phage types DT104, U302 and DT120 and cluster II associated to DT193 and U288. The results of this present study showed that MLVA is highly discriminatory and permitted the identification of identical profiles among isolates obtained at different points of the pork food chain. The same MLVA profile was observed in some cases among isolates with different phage types. While this can be explained by the fact that some phage types are closely related, it also indicates that combining phage typing and MLVA enhances strain typing of S. typhimurium.

Antifungal susceptibility testing and candidaemia at a tertiary referral hospital.

Candidaemia is associated with a high mortality. We have reviewed cases of candidaemia over a 2-year period at a tertiary referral hospital in association with the introduction of routine antifungal susceptibility testing. The aim of the study was two fold; firstly to establish the typical profile of a patient who might experience a Candida bloodstream infection and secondly, to evaluate methods of antifungal susceptibility testing. In 2008-2009, 31 patients with candidaemia were retrospectively identified using the Laboratory Information Systems (Apex). Clinical data were obtained by chart review. Antifungal susceptibility testing to fluconazole and voriconazole was carried out on 20 of the clinical isolates using three different methods. These isolates were also sent to the mycology reference laboratory at Bristol and results were compared. The male-to-female ratio was 2.1:1 with an age range from 6 weeks to 89 years. Candida albicans was the predominant species (n= 17). Patients were predominantly general surgical (39%), oncology (16%) and urology (13%). Identified risk factors included treatment with broad-spectrum antimicrobial agents (89%), central venous catheters (CVCs) (89%), and surgery during the current admission (54%). The crude mortality rate (death prior to discharge) was 42%. Only 1 of the 20 isolates tested, a Candida glabrata, tested resistant to fluconazole. Of 3 antifungal susceptibility test systems evaluated (VITEK 2, TREK Sensititre YeastOne and CLSI disk diffusion); the VITEK 2 system was considered most appropriate for routine use in our laboratory. Retrospective review of therapy identified 7 patients treated with echinocandins in whom susceptibility testing indicated that fluconazole could have been used with significant reduction in cost of therapy.