Martin Cormican

Verified

Martin verified their affiliation via an institutional email.

Learn more

Verified

Martin verified their affiliation via an institutional email.

Learn more

• MD
• Professor at Ollscoil na Gaillimhe – University of Galway

This report summarises available information on antimicrobial consumption and antimicrobial resistance in Ireland in the years 2017-2018. The report takes a One Health approach presenting human, animal and environmental information. The follows from a previous report for 2016.

Hypervirulent Klebsiella pneumoniae (hv Kp ) has emerged as a pathogen of global concern associated with invasive community-acquired infections. The combination of hypervirulence and carbapenem resistance can result in severe and difficult-to-treat infections. This retrospective study aimed to investigate the spread of hv Kp sequence type 23 (ST23)...

Consequences of Shiga toxin-producing Escherichia coli (STEC) infection can range in severity from asymptomatic infection to haemolytic uraemic syndrome (HUS), renal failure, and death. Groundwater-derived drinking water is an important route for STEC transmission. Detection of STEC in water is crucial for timely response and public health interven...

Background In February 2022, the United Kingdom (UK) detected a cluster of monophasic Salmonella Typhimurium based on whole genome sequencing (WGS). Subsequently, several countries reported cases belonging to this cluster. Epidemiological, microbiological and traceability investigations pointed toward a chocolate food business operator (FBO) in Bel...

Paratyphoid B fever (PTB) is caused by an invasive lineage (phylogroup 1, PG1) of Salmonella enterica serotype Paratyphi B (SPB). However, little was known about the global population structure, geographic distribution, and evolution of this pathogen. Here, we report a whole-genome analysis of 568 historical and contemporary SPB PG1 isolates, obtai...

Carbapenemase-producing Enterobacterales (CPE) is a diverse group of often multidrug-resistant organisms. Surveillance and control of infections are complicated due to the inter-species spread of carbapenemase-encoding genes (CEGs) on mobile genetic elements (MGEs), including plasmids and transposons. Due to wastewater discharges, urban water ecosy...

Clostridioides difficile PCR ribotype (RT) 002 is the second most prevalent RT in the Netherlands. In 2019, an increase in C. difficile infections (CDI) due to a clonal RT002 strains was reported in Ireland. In retrospect, a significant increase in the proportion of CDI due to RT002 was detected in the Netherlands between May 2017- May 2018 (11.9%...

Analysis of 594 isolates of Escherichia coli sequence type (ST)131 and its single locus variants carrying carbapenemase genes from 17 European Union/European Economic Area countries revealed acquisition of 18 carbapenemase variants, mainly in ST131 clades A and C. Most frequent were bla OXA-244 (n = 230) and bla OXA-48 (n = 224), detected in 14 and...

Executive summary Food supplements are defined in European Union (EU) food law (Directive 2002/46/EC, S.I. No. 506 of 2007) as “foodstuffs the purpose of which is to supplement the normal diet and which are concentrated sources of nutrients or other substances with a nutritional or physiological effect, alone or in combination, marketed in dose for...

Background The processing of blood cultures is technically difficult and time consuming. Nucleic acid amplification tests (NAATs) can supplement this process, with some commercial systems offering NAAT for multiple pathogens simultaneously. These platforms also present distinct challenges, including managing false positive identifications. The use...

What did you want to address in this study and why? In bacteria, NDM production can confer drug resistance and NDM-encoding genes can occur on mobile genetic elements, e.g. plasmids. The war in Ukraine has led Ukrainian people to migrate within Europe. Since March 2022, Ukrainian patients with, or affected by, drug-resistant bacteria have been det...

Paratyphoid B fever (PTB) is caused by an invasive lineage (phylogroup 1, PG1) of Salmonella enterica serotype Paratyphi B (SPB). Here, we provide a genomic overview of the population structure, geographic distribution, and evolution of SPB PG1 by analysing genomes from 568 historical and contemporary isolates, obtained globally, between 1898 and 2...

The major determinant of blood culture (BC) diagnostic performance is blood volume, and pediatric sample volumes are frequently low. We aimed to assess BC volumes in our institution, design an intervention to increase volumes, and assess its impact. All pediatric BCs submitted over a 7-month period to the microbiology laboratory in a university hos...

Escherichia coli is the predominant urinary pathogen in children. Irish and international studies have demonstrated increasing antimicrobial resistance (AMR) to antibiotics such as co-amoxiclav. We aimed to (1) examine the AMR patterns of paediatric urinary E. coli isolates, from both hospital and community sources, over a 10-year period; (2) asses...

Antimicrobial resistance (AMR) is recognised worldwide as one of the greatest threats to human health. Often referred to as the silent pandemic, AMR not only impacts on human health but has major implications for our animals, food production systems, environment and economy. The One Health concept recognises that the health of humans, animals and o...

Background In March 2022, an outbreak investigation was initiated in Ireland after identifying a cluster of monophasic Salmonella Typimurium cases, affecting primarily small children. Microbiological investigations revealed that the cluster was part of a wider international outbreak. Methods A total of 18 Irish outbreak cases were identified. We u...

Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we pro...

Go raibh maith agaibh as cuireadh a thabhairt dom labhairt libh maidin inniu faoin bpaindéim. Is iad na príomhphointí atá agam daoibhse agus do gach duine a bhfuil sásta éisteacht liom ná go bhfuil seans an-mhaith go dtiocfaidh frídín eile ar an bhfód amach anseo a scaipeann ar fud an domhain agus go mbeidh sé chomh dona le, nó b'fhéidir níos measa...

Whole genome sequencing data of 874 Escherichia coli isolates carrying bla NDM-5 from 13 European Union/European Economic Area countries between 2012 and June 2022 showed the predominance of sequence types ST167, ST405, ST410, ST361 and ST648, and an increasing frequency of detection. Nearly a third (30.6%) of these isolates were associated with in...

Understanding the role of exposure to natural recreational waters in the acquisition and transmission of antimicrobial resistance (AMR) is an area of increasing interest. A point prevalence study was carried out in the island of Ireland to determine the prevalence of colonisation with extended-spectrum beta-lactamase-producing Enterobacterales (ESB...

The second and third decades of the twenty-first century are marked by a flourishing of space technology which may soon realise human aspirations of a permanent multiplanetary presence. The prevention, control and management of infection with microbial pathogens is likely to play a key role in how successful human space aspirations will become. Thi...

The emergence and dissemination of mobile colistin resistance (mcr) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environmental samples (157 water and 157 wastewater) were collected in Ireland between 2018 and 2020. Samples collecte...

The spread of carbapenemase-producing Enterobacterales (CPE) is of major public health concern. The transmission dynamics of CPE in hospitals, particularly at the national level, are not well understood. Here, we describe a retrospective nationwide genomic surveillance study of CPE in Ireland between 2012 and 2017. We sequenced 746 national surveil...

Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries...

Background: Uncomplicated urinary tract infections (UTIs) are among the most common presentations of bacterial infections in the outpatient setting. The variation of outcomes reported in trials to assess the most effective treatment interventions for uncomplicated UTIs has meant that comparing and synthesising the outcomes across trials is challeng...

Hypervirulent Klebsiella pneumoniae has typically been associated with invasive, community-associated infections. This study describes the molecular, epidemiological and clinical characteristics of a cluster of carbapenemase-producing hypervirulent K. pneumoniae in the South-East of Ireland. It highlights the increasing risk that hypervirulent K. p...

Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries...

This paper represents a reflection on the response to the COVID-19 pandemic in Ireland

The emergence and dissemination of mobile colistin resistance ( mcr ) genes across the globe poses a significant threat to public health, as colistin remains one of the last line treatment options for multi-drug resistant infections. Environmental samples (157 water and 157 wastewater) were collected in Ireland between 2018 and 2020. Samples collec...

Background: Uncomplicated urinary tract infections (UTIs) are amongst the most frequent infections presenting in the outpatient setting. A growing number of clinical trials are assessing the most effective treatment interventions for uncomplicated UTI. Due to the heterogeneity of the outcomes reported in these trials, however, comparing these outc...

Carbapenemase-producing Enterobacterales (CPE) are important globally. In 2017, Ireland declared a national public health emergency to address CPE in acute hospitals. A National Public Health Emergency Team and an expert advisory group (EAG) were established. The EAG has identified key learnings to inform future strategies. First, there is still an...

The natural environment represents a complex reservoir of antibiotic-resistant bacteria as a consequence of different wastewater discharges including anthropogenic and agricultural. Therefore, the aim of this study was to examine sewage and waters across Ireland for the presence of antibiotic-resistant Enterobacterales. Samples were collected from...

p>The Acknowledgements section in the original version of this Article was incomplete. “This study has received funding from the European Union’s Horizon 2020 research and innovation program under Grant agreement no. 643476 (COMPARE), the World Health Organization, and The Novo Nordisk Foundation (NNF16OC0021856: Global Surveillance of Antimicrobia...

Water bodies worldwide have proven to be vast reservoirs of clinically significant antibiotic resistant organisms. Contamination of waters by anthropogenic discharges is a significant contributor to the widespread dissemination of antibiotic resistance. The aim of this research was to investigate multiple different anthropogenic sources on a nation...

Objectives To describe the epidemiology, age at infection, clinical characteristics and outcome of listeria infection in young infants to inform management and empiric antibiotic choice in young infants. Design Prospective 2-year surveillance of Listeria monocytogenes infection in young infants detected through the British Paediatric Surveillance...

We present a PCR assay screening Chlamydia trachomatis directly from urine without pre-amplification or sample clean-up and demonstrate suitability for implementation on a disposable cartridge system. Primers and probes were designed to detect all Chlamydia trachomatis serovars with a high degree of sensitivity and specificity. The assay also incor...

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 cultur...

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 a...

Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptile...

BACKGROUND Urinary tract infections (UTI) are one of the most common conditions in females. Current information on presentation, management and natural course of the infection is based on paper diaries filled out by patients and subsequently posted. OBJECTIVE The aim of the study was to explore the feasibility of a smartphone app to assess the nat...

Background: Urinary tract infections (UTIs) are one of the most common conditions in women. Current information on the presentation, management, and natural course of the infection is based on paper diaries filled out and subsequently posted by patients. Objective: The aim of this study is to explore the feasibility of a smartphone app to assess...

Background Urinary tract infections (UTI) are one of the most common conditions in females. Current information on presentation, management and natural course of the infection is based on paper diaries filled out by patients and subsequently posted. The aim of the study was to explore the feasibility of a smartphone app to assess the natural course...

Background: Most publicly available genomes of Salmonella enterica are from human disease in the US and the UK, or from domesticated animals in the US. Methods: Here we describe a historical collection of 10,000 strains isolated between 1891-2010 in 73 different countries. They encompass a broad range of sources, ranging from rivers through reptile...

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potenti...

Analysis of sequencing data for 143 blaNDM-1- and blaOXA-48-positive Klebsiella pneumoniae isolates from 13 European national collections and the public domain resulted in the identification of 15 previously undetected multi-country transmission clusters. For 10 clusters, cases had prior travel/hospitalisation history in countries outside of the Eu...

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 establishe...

Escherichia coli sequence type 131 (ST131) is a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. Here, we investigated an outbreak of E. coli ST131 producing extended spectrum β-lactamases (ESBLs) in a long-term care facility (LTCF) in Ireland by combining data from this LTCF (n=69) with other Irish (n=35)...

Antimicrobial resistance (AMR) poses a threat to public health. Clinical microbiology laboratories typically rely on culturing bacteria for antimicrobial-susceptibility testing (AST). As the implementation costs and technical barriers fall, whole-genome sequencing (WGS) has emerged as a 'one-stop' test for epidemiological and predictive AST results...

PIER: Public health Impact of Exposure to antibiotic Resistance in recreational water

Shigella sonnei increasingly dominates the international epidemiological landscape of shigellosis. Treatment options for S. sonnei are dwindling due to resistance to several key antimicrobials, including the fluoroquinolones. Here we analyse nearly 400 S. sonnei whole genome sequences from both endemic and non-endemic regions to delineate the evolu...

Escherichia coli sequence type 131 (ST131) is a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. Here, we investigated an outbreak of E. coli ST131 producing extended spectrum β-lactamases (ESBLs) in a long-term care facility (LTCF) in Ireland by combining data from this LTCF (n=69) with other Irish (n=35)...

Background: Antimicrobial resistance (AMR) poses a threat to public health. Clinical microbiology laboratories typically rely on culturing bacteria for antimicrobial susceptibility testing (AST). As the implementation costs and technical barriers fall, whole-genome sequencing (WGS) has emerged as a one-stop test for epidemiological and predictive A...

Objectives: The prevalence of infections caused by OXA-48-like carbapenemase-producing organisms in Ireland has increased dramatically since 2011 and is an urgent public health issue. Genome-based high-resolution genotyping was used to analyse clinical isolates submitted to the Irish Carbapenemase-Producing Enterobacteriaceae Reference Laboratory...

Antimicrobial resistance is a major public health concern. Carbapenemase-producing Enterobacterales (CPE) represent a significant health threat as some strains are resistant to almost all available antibiotics. The aim of this research was to examine hospital effluent and municipal wastewater in an urban area in Ireland for CPE. Samples of hospital...

Background: In general practice, many infections are treated empirically prior to or without microbiological confirmation. Prediction of antimicrobial susceptibility could optimise prescribing thus improving patient outcomes. Decision tree models are a novel idea to predict AMR at the time of clinical presentation. This study aims to apply a predi...

Background The SENTRY Antimicrobial Surveillance Program was established in 1997 and presently encompasses more than 750 000 bacterial isolates from over 400 medical centers worldwide. Among these pathogens, enterococci represents a prominent cause of bloodstream (BSIs), intra-abdominal (IAIs), skin and skin structure, and urinary tract infections...

Background Long-term care facilities (LTCFs) are important locations of antimicrobial consumption. Of particular concern is inappropriate prescribing of prophylactic antimicrobials. AimWe aimed to explore factors related to antimicrobial prophylaxis in LTCFs in Ireland. Methods The point prevalence surveys of Healthcare-Associated Infections in Lon...

Cronobacter sakazakii has been documented as a cause of life-threating infections, predominantly in neonates. We conducted a multicenter study to assess the occurrence of C. sakazakii across Europe and the extent of clonality for outbreak detection. National coordinators representing 24 countries in Europe were requested to submit all human C. saka...

Background Urinary tract infections (UTIs) are the second most common infection presenting in the community. Clinical guidelines and decision aids assist health practitioners to treat a UTI; however, treatment practices vary due to patient needs and context of presentation. Numerous trials have evaluated the effectiveness of treatment interventions...

In 2017, an outbreak of gastroenteritis in England attributed to Salmonella Adjame was detected and investigated. With the introduction of whole genome sequencing (WGS) for microbial typing, methods for comparing international outbreak data require evaluation. A case was defined as a person resident in England with a clinical sample from 1 June 201...

Silver nanoparticles (AgNPs), due to their antibacterial activity, have been incorporated into numerous consumer products. Their environmental impact however, is currently unclear. Uncertainties surround the concentration, fate, and effects of AgNPs in aquatic environments. This study examined the suitability of activated charcoal as a capture mate...

Background/objectives: Broad-spectrum, second-line antimicrobials may be prescribed when initial first-line options prove ineffective. This study compares prescribing practices and identifies potential influencing factors for first- and second-line antimicrobials in long-term care facilities. Design: Point prevalence survey of health care-associ...

Background The 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 gathe...

Background and aim The trend in reported case counts of invasive Listeria monocytogenes ( Lm ), a potentially severe food-borne disease, has been increasing since 2008. In 2015, 2,224 cases were reported in the European Union/European Economic Area (EU/EEA). We aimed to validate the microbiological and epidemiological aspects of an envisaged EU/EEA...

Shiga toxigenic Escherichia coli (STEC) are pathogenic E. coli that cause infectious diarrhoea. In some cases infection may be complicated by renal failure and death. The incidence of human infection with STEC in Ireland is the highest in Europe. The objective of the study was to examine the spatial incidence of human STEC infection in a region of...

Background: Fluoroquinolones (FQs) are second line antimicrobial agents. Once the decision to prescribe an antimicrobial is made, its choice should be based on both the benefits and harms. This systematic review quantifies the occurrence of common adverse events (AEs) related to FQs in relation to any other antimicrobial for any indication in prim...

Listeria monocytogenes is a major human foodborne pathogen that is prevalent in the natural environment and has a high case fatality rate. Whole genome sequencing (WGS) analysis has emerged as a valuable methodology for the classification of L. monocytogenes isolates and the identification of virulence islands that may influence infectivity. In thi...

Bacterial meningitis infection is a leading global health concern for which rapid and accurate diagnosis is essential to reduce associated morbidity and mortality. Loop-mediated isothermal amplification (LAMP) offers an effective low-cost diagnostic approach; however, multiplex LAMP is difficult to achieve, limiting its application. We have develop...

Recombinase polymerase amplification (RPA) is an isothermal nucleic acid amplification technology that provides rapid and robust infectious disease pathogen detection, ideal for point-of-care (POC) diagnostics in disease-prevalent low-resource countries. We have developed and evaluated three duplex RPA assays incorporating competitive internal cont...

Immunocompromised patients are at risk of invasive fungal infection. These high-risk patients are nursed in protective isolation to reduce the risk of nosocomial aspergillosis while in hospital-ideally in a positive pressure single room with high-efficiency particulate air filtration. However, neutral pressure rooms are a potential alternative, esp...

This study aimed to provide new insights into the epidemiology of Salmonella in pig production, focusing on potential shedding patterns in breeding pigs throughout a full production cycle and the risk of transmission of infection from the sow to her offspring. A longitudinal study was conducted on five farrow-to-finish commercial pig farms. In each...

Background: Lyme borreliosis is caused by Borrelia burgdorferi and is the most common tick-transmitted infection in temperate regions. Infection often presents with erythema migrans and/or other clinical features in early infection. Methods: Blood samples are submitted for testing for antibodies to Borrelia burgdorferi by enzyme immunoassay and...

In 2007, a waterborne outbreak of Cryptosporidium hominis infection occurred in western Ireland, resulting in 242 laboratory-confirmed cases and an uncertain number of unconfirmed cases. A boil water notice was in place for 158 days that affected 120,432 persons residing in the area, businesses, visitors, and commuters. This outbreak represented th...

ECDC, EFSA and EMA have jointly established a list of harmonised outcome indicators to assist EU Member States in assessing their progress in reducing the use of antimicrobials and antimicrobial resistance (AMR) in both humans and food-producing animals. The proposed indicators have been selected on the basis of data collected by Member States at t...

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, Sp...