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.

Attitudes and practices of Irish hospital-based physicians towards hand hygiene and hand rubbing using alcohol-based hand rub: a comparison between 2007 and 2015.

BACKGROUND: Hand hygiene is the cornerstone of infection prevention and control practices, and reduces healthcare-associated infections significantly. However, international evidence suggests that medical doctors demonstrate poor compliance. AIM: To explore and compare practices and attitudes towards hand hygiene, particularly hand rubbing using alcohol-based hand rub (ABHR), among hospital-based physicians in Ireland between 2007 and 2015. METHODS: In 2007, a random sample of doctors in a large teaching hospital was invited to complete a postal survey using a validated questionnaire. In 2015, the study was replicated among all doctors employed in a university hospital group, including the setting of the original study, using an online survey. Data were analysed using SPSS and Survey Monkey. FINDINGS: Predominately positive and improving attitudes and practices were found, with 86% of doctors compliant with hand hygiene before patient contact in 2015, compared with 58% in 2007. Ninety-one percent of doctors were compliant after patient contact in 2015, compared with 76% in 2007. In 2015, only 39% of respondents reported that they 'almost always' used ABHR for hand hygiene. However, this represents 13.5% more than in 2007. Stated barriers to use of ABHR included dermatological issues, poor acceptance, tolerance and poor availability of ABHR products. CONCLUSION: Greater awareness of hand hygiene guidelines and greater governance appear to have had a positive impact on practice. However, despite this, practice remains suboptimal and there is scope for substantial improvement. Continued and sustained efforts are required in order to build on progress achieved since the World Health Organization hand hygiene guidelines were published in 2009.

An Irish outbreak of New Delhi metallo-ß-lactamase (NDM)-1 carbapenemase-producing Enterobacteriaceae: increasing but unrecognized prevalence.

BACKGROUND: Carbapenemase-producing Enterobacteriaceae (CPE) may cause healthcare-associated infections with high mortality rates. New Delhi metallo-ß-lactamase-1 (NDM-1) is among the most recently discovered carbapenemases. AIM: To report the first outbreak of NDM-1 CPE in Ireland, including microbiological and epidemiological characteristics, and assessing the impact of infection prevention and control measures. METHODS: This was a retrospective microbiological and epidemiological review. Cases were defined as patients with a CPE-positive culture. Contacts were designated as roommates or ward mates. FINDINGS: This outbreak involved 10 patients with a median age of 71 years (range: 45-90), located in three separate but affiliated healthcare facilities. One patient was infected (the index case); the nine others were colonized. Nine NDM-1-producing Klebsiella pneumoniae, an NDM-1-producing Escherichia coli and a K. pneumoniae carbapenemase (KPC)-producing Enterobacter cloacae were detected between week 24, 2014 and week 37, 2014. Pulsed-field gel electrophoresis demonstrated similarity. NDM-1-positive isolates were meropenem resistant with minimum inhibitory concentrations (MICs) ranging from 12 to 32 µg/mL. All were tigecycline susceptible (MICs ≤1 µg/mL). One isolate was colistin resistant (MIC 4.0 µg/mL; mcr-1 gene not detected). In 2015, four further NDM-1 isolates were detected. CONCLUSION: The successful management of this outbreak was achieved via the prompt implementation of enhanced infection prevention and control practices to prevent transmission. These patients did not have a history of travel outside of Ireland, but several had frequent hospitalizations in Ireland, raising concerns regarding the possibility of increasing but unrecognized prevalence of NDM-1 and potential decline in value of travel history as a marker of colonization risk.

Combined education and skin antisepsis intervention for persistently high blood-culture contamination rates in neonatal intensive care.

Contaminated blood cultures represent challenges regarding diagnosis, duration of hospitalization, antimicrobial use, pharmacy and laboratory costs. Facing problematic neonatal blood culture contamination (3.8%), we instigated a successful intervention combining skin antisepsis using sterile applicators with 2% chlorhexidine gluconate in 70% isopropanol prior to phlebotomy (replacing 70% isopropanol) and staff education. In the six months prior to intervention, 364 neonatal peripheral blood samples were collected. Fourteen (3.8%) were contaminated. In the post-intervention six months, 314 samples were collected. Three (0.96%) were contaminated, representing significant improvement (Fisher's exact test: P = 0.0259). No dermatological sequelae were observed. The improvement has been sustained.

The incidence of S. aureus bacteraemia in acute hospitals of the Mid-Western Area, Ireland, 2002-2004.

Concerns about healthcare-associated infections and the global crisis in antimicrobial resistance has combined to accentuate the fears around so-called "superbugs". In Ireland there is no single agreed indicator regarded as a true measure of the level of methicillin resistant Staphylococcus aureus (MRSA) in hospitals. The objective of this study was to compare two crude measures of MRSA--the percentage of bacteraemia caused by MRSA and the incidence rate (per 1000 bed days used) of MRSA bacteraemia in six acute hospitals. We examined all blood cultures positive for S. aureus (methicillin sensitive and resistant) from 2002 to 2004 in the Health Service Executive (HSE) Mid-Western Area of Ireland. Hospital In-Patient Enquiry (HIPE) data was used to determine monthly in-patient bed days used. Of 245 patient episodes of bacteraemia, 119 were MRSA. The trends in the percentage of isolates that were MRSA and the incidence rate calculated were compared. The incidence rate appears to be a more reliable and robust indicator of MRSA in hospitals than the percentage. Despite many difficulties in interpreting indicators of MRSA they should not preclude the regular publication of data at least at regional level in Ireland.

The incidence of S. aureus bacteraemia in acute hospitals of the Mid-Western Area, Ireland, 2002-2004.

Concerns about healthcare-associated infections and the global crisis in antimicrobial resistance has combined to accentuate the fears around so-called "superbugs". In Ireland there is no single agreed indicator regarded as a true measure of the level of methicillin resistant Staphylococcus aureus (MRSA) in hospitals. The objective of this study was to compare two crude measures of MRSA - the percentage of bacteraemia caused by MRSA and the incidence rate (per 1000 bed days used) of MRSA bacteraemia in six acute hospitals. We examined all blood cultures positive for S. aureus (methicillin sensitive and resistant) from 2002 to 2004 in the Health Service Executive (HSE) Mid-Western Area of Ireland. Hospital In-Patient Enquiry (HIPE) data was used to determine monthly in-patient bed days used. Of 245 patient episodes of bacteraemia, 119 were MRSA. The trends in the percentage of isolates that were MRSA and the incidence rate calculated were compared. The incidence rate appears to be a more reliable and robust indicator of MRSA in hospitals than the percentage. Despite many difficulties in interpreting indicators of MRSA they should not preclude the regular publication of data at least at regional level in Ireland.

Twenty four hour oesophageal acidity in achalasia before and after pneumatic dilatation.

Radiotelemetric ambulatory 24 hour oesophageal pH measurement was carried out in 17 patients with symptomatic manometrically proven achalasia before and after pneumatic dilatation. Before dilatation an abnormally high percentage acid exposure time was present but typical episodes of gastro-oesophageal reflux occurred in only one patient. In nine patients who had a oesophageal food residue these values were significantly greater than those found in the remaining patients without retained food. Analysis of oesophageal food residues revealed that the low pH was predominantly caused by lactic acid. These findings indicate that preoperative oesophageal pH studies do not offer a valid means of selection of patients in whom an antireflux procedure should be combined with cardiomyotomy. Repeat studies one week after pneumatic dilatation showed a fall in the acid exposure time in patients with initial food residue presumably resulting from improved oesophageal emptying after treatment. A significant rise in acid exposure time after dilatation was seen in those patients without initial food residue presumably resulting from gastro-oesophageal reflux after therapeutic disruption of the lower oesophageal sphincter. Troublesome symptoms of gastro-oesophageal reflux were, however, uncommon after bag dilatation.