A novel characterized multi-drug-resistant Pseudocitrobacter sp. isolated from a patient colonized while admitted to a tertiary teaching hospital.

BACKGROUND: Reports of nosocomial infections typically describe recognised microorganisms. Here, a novel bacterial species was isolated, based on rectal swab screening for carbapenemases post-admission, then phenotypically and genetically characterized. METHODS: Sensititre, Vitek and API kits, MALDI and Illumina MiSeq were employed before profiles and phylogeny were compared with other related species. FINDINGS: Determined to be a possible Enterobacterales, the isolate was found to have 99.7% 16s rRNA identity to Pseudocitrobacter corydidari; an Asian cockroach-associated species. Given the highly conserved/low variability of 16S rRNA genes in Enterobacterales, average nucleotide identity (ANI) analysis compared the new isolate's genome with those of 18 Enterobacteriaceae species, including confirmed species of Pseudocitrobacter and unnamed Pseudocitrobacter species in the SILVA database. Of these, Pseudocitrobactercorydidari had the highest ANI at 0.9562. The published genome of the only known isolate of P.corydidari does not include Antimicrobial Resistance Genes (ARGs), with exception of potential drug efflux transporters. In contrast, our clinical isolate bears recognised antimicrobial resistance genes, including Klebsiella pneumoniae carbapenemase. The associated genome suggests resistance to carbapenems, ß-lactams, sulfonamides, fluoroquinolones, macrolides, aminoglycosides and cephalosporins. Phenotypic antimicrobial resistance was confirmed. CONCLUSION: Evident variations in ARG profiles, human colonization and origin in a clinically relevant niche that is geographically, physically and chemically disparate lend credibility for divergent evolution or, less likely, parallel evolution with P. corydidari. Genome data for this new species have been submitted to GENBANK using the proposed nomenclature Pseudocitrobacter limerickensis. The patient was colonized, rather than infected, and did not require antimicrobial treatment.

Large-scale characterization of hospital wastewater system microbiomes and clinical isolates from infected patients: profiling of multi-drug-resistant microbial species.

BACKGROUND: Hospital-acquired infections (HAIs) and infectious agents exhibiting antimicrobial resistance (AMR) are challenges globally. Environmental patient-facing wastewater apparatus including handwashing sinks, showers and toilets are increasingly identified as sources of infectious agents and AMR genes. AIM: To provide large-scale metagenomics analysis of wastewater systems in a large teaching hospital in the Republic of Ireland experiencing multi-drug-resistant HAI outbreaks. METHODS: Wastewater pipe sections (N=20) were removed immediately prior to refurbishment of a medical ward where HAIs had been endemic. These comprised toilet U-bends, and sink and shower drains. Following DNA extraction, each pipe section underwent metagenomic analysis. FINDINGS: Diverse taxonomic and resistome profiles were observed, with members of phyla Proteobacteria and Actinobacteria dominating (38.23 ± 5.68% and 15.78 ± 3.53%, respectively). Genomes of five clinical isolates were analysed. These AMR bacterial isolates were from patients >48 h post-admission to the ward. Genomic analysis determined that the isolates bore a high number of antimicrobial resistance genes (ARGs). CONCLUSION: Comparison of resistome profiles of isolates and wastewater metagenomes revealed high degrees of similarity, with many identical ARGs shared, suggesting probable acquisition post-admission. The highest numbers of ARGs observed were those encoding resistance to clinically significant and commonly used antibiotic classes. Average nucleotide identity analysis confirmed the presence of highly similar or identical genomes in clinical isolates and wastewater pipes. These unique large-scale analyses reinforce the need for regular cleaning and decontamination of patient-facing hospital wastewater pipes and effective infection control policies to prevent transmission of nosocomial infection and emergence of AMR within potential wastewater reservoirs.

Microbial epidemiology and clinical risk factors of carbapenemase-producing Enterobacterales amongst Irish patients from first detection in 2009 until 2020.

Background: Carbapenemase producing Enterobacterales (CPE) are major public health threats. Aim: To review microbial epidemiology of CPE, as well as clinical risk factors and infections, amongst CPE positive patients over 12 years in an Irish tertiary hospital. Methods: Retrospective observational study of data extracted from a laboratory CPE database, electronic healthcare records and manual review of patient charts. Common risk factors, treatment regimens for all CPE related infections, and clinical outcomes were ascertained. Findings: Among CPE strains isolated from 460 patients, Klebsiella pneumoniae carbapenemase (KPC) was the carbapenemase most frequently detected, accounting for 87.4% (459) of all CPE enzymes. Citrobacter species 177 (33.7%) were the most common species harbouring this enzyme. 428 CPE positive patients (93%) were identified in the acute hospital setting; the most common risk factor for CPE acquisition was history of hospitalisation, observed in 305 (66%) cases. Thirty patients (6.5%) had confirmed infections post-acquisition, of which four were bloodstream infections. There were 19 subsequent episodes of non CPE-related bacteraemia in this cohort. All causal mortality at 30 days was 41 patients (8.9%). However, clinical review determined that CPE was an indirect associative factor in 8 patient deaths. Conclusions: In this tertiary hospital setting, microbial epidemiology is changing; with both OXA-48 enzymes and KPC-producing Citrobacter species becoming more prevalent. Whilst the burden of CPE related infections, especially bacteraemia, was low over the study period, it remains critical that basic infection prevention and control practices are adhered to lest the observed changes in epidemiology result in an increase in clinical manifestations.

Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole-genome sequencing.

AIM: To provide a detailed genomic-epidemiological description of a complex multi-ward SARS-CoV-2 outbreak, which originated in the crowded emergency department (ED) in our hospital during the third wave of the COVID-19 pandemic, and was elucidated promptly by local whole-genome sequencing (WGS). METHODS: SARS-CoV-2 was detected by reverse transcriptase real-time polymerase chain reaction on viral RNA extracted from nasopharyngeal swabs. WGS was performed using an Oxford MinION Mk1C instrument following the ARTIC v3 sequencing protocol. High-quality consensus genomes were assembled with the artic-ncov2019 bioinformatics pipeline and viral phylogenetic trees were built, inferred by maximum-likelihood. Clusters were defined using a threshold of 0-1 single nucleotide polymorphisms (SNPs) between epidemiologically linked sequences. RESULTS: In April 2021, outbreaks of COVID-19 were declared on two wards at University Hospital Limerick after 4 healthcare-associated SARS-CoV-2 infections were detected by post-admission surveillance testing. Contact tracing identified 12 further connected cases; all with direct or indirect links to the ED 'COVID Zone'. All sequences were assigned to the Pangolin B.1.1.7 lineage by WGS, and SNP-level analysis revealed two distinct but simultaneous clusters of infections. Repeated transmission in the ED was demonstrated, involving patients accommodated on trolleys in crowded areas, resulting in multiple generations of infections across three inpatient hospital wards and subsequently to the local community. These findings informed mitigation efforts to prevent cross-transmission in the ED. CONCLUSION: Cross-transmission of SARS-CoV-2 occurred repeatedly in an overcrowded emergency department. Viral WGS elucidated complex viral transmission networks in our hospital and informed infection, prevention and control practice.

Association between tocilizumab treatment of hyperinflammatory patients with COVID-19 in a critical care setting and elevated incidence of hospital-acquired bacterial and invasive fungal infections.

BACKGROUND: Tocilizumab is an interleukin-6 inhibitor that reduces mortality and the need for invasive mechanical ventilation, while increasing the possibility of successful hospital discharge for hyperinflammatory patients with severe coronavirus disease 2019 (COVID-19). No increase in adverse events or serious infections has been reported previously. AIM: To describe the characteristics and outcomes of patients with severe COVID-19 in critical care who received tocilizumab, and to compare mortality and length of hospital stay for patients who received tocilizumab (N=41) with those who did not (N=33). METHODS: Retrospective review of data related to patients with COVID-19 who received tocilizumab in a critical care setting from 1st January to 31st December 2021. FINDINGS: Amongst COVID-19 survivors, those who had received tocilizumab had longer intensive care unit (ICU) stays (median length 21 vs 9 days) and hospital stays (45 vs 34 days) compared with those who had not received tocilizumab. Thirty-day mortality (29% vs 36%; P=0.5196) and 60-day mortality (37% and 42%; P=0.6138) were not significantly lower in patients who received tocilizumab. Serious bacterial and fungal infections occurred at higher frequency amongst patients who received tocilizumab [odds ratio (OR) 2.67, 95% confidence interval (CI) 1.04-6.86; P=0.042], and at significantly higher frequency than in non-COVID-19 ICU admissions (OR 5.26, 95% CI 3.08-9.00; P<0.0001). CONCLUSIONS: In this single-centre study, patients in critical care with severe COVID-19 who received tocilizumab had a greater number of serious bacterial and fungal infections, but this may not have been a direct effect of tocilizumab treatment.

Assessment of the microbial load of airway clearance devices used by a cohort of children with cystic fibrosis.

BACKGROUND: Positive expiratory pressure (PEP) devices are an important element of the management of cystic fibrosis, and of other respiratory diseases. Whereas there have been reports in the literature of contamination of airway clearance devices and their surfaces by microbial pathogens, there is little evidence available regarding such contamination and its contribution to respiratory infection. AIM: To establish whether pathogenic bacteria can contaminate PEP devices in the context of normal cleaning and maintenance practices. METHODS: Patients' home-use clearance devices were brought to a routine clinic appointment and collected for microbiology sampling and analysis. The patients were provided with replacement devices. Nineteen such devices were collected from 17 patients, reflecting use of multiple devices by some patients. Swabs were taken and cultured from each patient's used device, the patient's airway, as well as from new unopened and unused devices that acted as controls. RESULTS: Seven of 19 devices (37%) tested positive for presence of pathogenic bacteria. Device-cleaning methods varied among patients and non-sterilization methods were found to be ineffective at removing pathogens. Microbial species found on the devices did not correlate with those identified from airway swabs. CONCLUSION: This study demonstrates the presence of pathogens on positive expiratory pressure devices. The potential for transmission of these pathogens to the patient's airway and the risk of infection remains unclear and requires further study.

Outcomes of point-of-care testing for influenza in the emergency department of a tertiary referral hospital in Ireland.

BACKGROUND: Seasonal influenza causes significant morbidity and mortality, and represents a recurring financial burden for community- and hospital-based treatment. Nosocomial outbreaks exacerbate the impact of influenza. Rapid diagnosis of influenza has been shown to reduce transmission. However, point-of-care testing (POCT) in emergency departments and prudent direction of patients with the virus to reduce hospital-acquired infection (HAI) have not been evaluated widely. AIM: To assess performance characteristics of the Abbott ID NOW™ Influenza A & B 2 system, impact on incidence of hospital-acquired influenza, and admission rate ratio for patients who have POCT compared with laboratory testing. POCT was introduced in the 2018-2019 influenza season. Data from then were compared with preceding and subsequent seasons. METHODS: Records of POCT and laboratory testing for the 2017-2018, 2018-2019, and 2019-2020 influenza seasons were analysed. Sensitivity and specificity of POCT were compared pairwise with Xpert Flu A/B/RSV. Patient admission rates and time of waiting for admission were compared. FINDINGS: Compared to laboratory assay, POCT demonstrated sensitivity of 90.6% (95% confidence interval (CI): 78.6-96.5) and specificity of 99.2% (95.2-100) for influenza A, with 51.4% and 41.9% reductions in numbers of HAIs observed in the two seasons when POCT was available, respectively. The admission rate ratio for influenza cases diagnosed by POCT compared with laboratory diagnosis was 0.72 (95% CI: 0.53-0.97; P = 0.031). CONCLUSION: POCT for influenza appears a feasible strategy for testing of patients during peak influenza virus season, with potential to reduce HAI. The relatively rapid turnaround time may also benefit clinical management of patients presenting at emergency departments with suspected influenza.

Time to positivity (TTP) of neonatal blood cultures: a trend analysis over a decade from Ireland.

Background and aims: Blood culture (BC) remains gold standard for the evaluation and diagnosis of neonatal sepsis. Time when BC becomes positive and the type of microorganism isolated are crucial in deciding the antimicrobial management. Likely pathogenicity of organisms growing in BC could potentially be predicted based on the "time to positivity" (TTP). We aimed to estimate the predictive value of isolating a likely pathogenic organism depending on TTP; evaluate the aetiological trend and neonatal mortality rate due to culture-proven neonatal sepsis for over a decade and verify whether the application of a "36 hour rule" to discontinue empiric antibiotics in well newborn infants with negative BC would be safe.Methods: Retrospective review of BC results over a 14-year period from a regional neonatal unit in Ireland. Laboratory data were independently extracted in relation to BC results from the laboratory information management system (LIMS-iLAB). Neonatal mortality data were collected from multiple sources. Statistical analysis included logistic regression, chi-square, and Mann-Whitney U-test.Results: Over a 14-year period 11,432 neonatal BC specimens were incubated of which 605 (5.3%) turned positive. Overall, the commonest organism grown was coagulase-negative Staphylococcus (CoNS), 416 (68.8%). Main pathogenic organisms were Staphylococcus aureus 23 (3.8%), Enterococcus spp. 22 (3.6%), E.coli 21 (3.5%), group B Streptococcus (GBS) 18 (3.0%), and Klebsiella species 9 (1.5%). Gram-negative organisms had the shortest TTP, with Klebsiella spp. having a median TTP of 10 h and E. coli 11 h. For Gram-positives, GBS had a median TTP of 12 h, Enterococcus species 14 h, with S. aureus growing at a median time of 15 h. All of the Klebsiella spp. and other Coliforms were detected within 24 h, with, 95.2% of E.coli, 94.4% of GBS, 95.5% of Enterococci, and 95.7% of S. aureus, flagging positive in 24 h. Using logistic regression the omnibus test of the coefficients in the resulting model was significant (p < .001). Our observed coefficient (ß) for TTP was 0.144; shorter the TTP higher was the likelihood of isolating a pathogenic organism, with an odds ratio (OR) of 1.155. We also report a relatively low blood culture proven sepsis-specific neonatal mortality rate of 0.403/1000 live births and in all such instances observed TTP was less than 24 h.Conclusion: Duration of this study exceeds that of most of the neonatal blood culture TTP analysis published to-date. A shorter TTP is an important adjunct to suggest the growth of a pathogenic organism while managing suspected neonatal sepsis. TTP if < 24 h per se would not necessarily confirm the growth of a highly pathogenic organism; however, if a positive growth is likely to happen for a significant neonatal pathogen, in more than 98% the TTP would be within 24 h. This offers the clinician more of negative predictive value than a positive one; when there is no growth in BC. Our observation on TTP reiterate the National Institute of Health and Care Excellence (NICE) guideline of discontinuation of empiric antibiotics after 36 h in and clinically well and BC negative newborn infants.

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.

Specialized cleaning associated with antimicrobial coatings for reduction of hospital-acquired infection: opinion of the COST Action Network AMiCI (CA15114).

Recognized issues with poor hand hygiene compliance among healthcare workers and reports of recontamination of previously chemically disinfected surfaces through hand contact emphasize the need for novel hygiene methods in addition to those currently available. One such approach involves antimicrobial (nano) coatings (AMCs), whereby integrated active ingredients are responsible for elimination of micro-organisms that come into contact with treated surfaces. While widely studied under laboratory conditions with promising results, studies under real-life healthcare conditions are scarce. The views of 75 contributors from 30 European countries were collated regarding specialized cleaning associated with AMCs for reduction of healthcare-associated infection. There was unanimous agreement that generation of scientific guidelines for cleaning of AMCs, using traditional or new processes, is needed. Specific topics included: understanding mechanisms of action of cleaning materials and their physical interactions with conventional coatings and AMCs; that assessments mimic the life cycle of coatings to determine the impact of repetitive cleaning and other aspects of ageing (e.g. exposure to sunlight); determining concentrations of AMC-derived biocides in effluents; and development of effective de-activation and sterilization treatments for cleaning effluents. Further, the consensus opinion was that, prior to widespread implementation of AMCs, there is a need for clarification of the varying responsibilities of involved clinical, healthcare management, cleaning services and environmental safety stakeholders.