David C Coleman

Trinity College Dublin | TCD · School of Dental Science

Background: Diabetic foot ulcer infections (DFUIs) are the leading cause of lower limb amputations, mediated predominantly by Staphylococcus aureus. pH neutral electrochemically-generated hypochlorous acid (anolyte) is a non-toxic, microbiocidal agent with significant potential for wound disinfection. Aims: To investigate both the effectiveness...

Background A novel Panton-Valentine leukocidin (PVL)-positive meticillin-resistant Staphylococcus aureus (MRSA) clonal complex (CC)5-MRSA-IVc (‘Sri Lankan’ clone) was recently described from Sri Lanka. Similar isolates caused a recent Irish hospital outbreak. Aims To investigate the international dissemination and diversity of PVL-positive CC5-MRS...

Community-associated, methicillin-resistant Staphylococcus aureus (MRSA) lineages have emerged in many geographically distinct regions around the world during the past 30 y. Here, we apply consistent phylodynamic methods across multiple community- associated MRSA lineages to describe and contrast their patterns of emergence and dis- semination. We...

Background Dental handpieces (DHPs) are reusable invasive medical devices that must be cleaned, decontaminated, lubricated and steam sterilized after use. DHPs have a complex internal design including narrow channels, contamination of which can compromise sterilization. DHPs are not designed for routine disassembly, making cleaning/decontamination...

Background The role of meticillin-resistant Staphylococcus aureus (MSSA) colonization of healthcare workers (HCWs), patients and the hospital environment in MSSA transmission events (TEs) is poorly understood. Aims We recently investigated these roles for MRSA under non-outbreak conditions in a large hospital with a history of endemic MRSA over tw...

Background Vancomycin-resistant Enterococcus faecium (VREfm) cause a wide range of hospital infections. Ireland has had one of the highest invasive VREfm infection rates in Europe over the last decade, yet little is known about Irish VREfm. Objectives To investigate the population structure of Irish VREfm, explore diversity by analysing the vanA t...

Background The role of MRSA colonization of healthcare workers (HCWs), patients and the hospital environment in MRSA transmission in non-outbreak settings is poorly understood. Aims To investigate transmission events (TEs) involving HCWs, patients and the environment under non-outbreak conditions in a hospital with a history of endemic MRSA using...

This study investigated the evolution and epidemiology of the community-associated and multidrug-resistant Staphylococcus aureus clone European CC1-MRSA-IV. Whole-genome sequences were obtained for 194 European CC1-MRSA-IV isolates (189 of human and 5 of animal origin) from 12 countries, and 10 meticillin-susceptible precursors (from North-Eastern...

Community-associated, methicillin-resistant Staphylococcus aureus (MRSA) lineages have emerged in many geographically distinct regions around the world during the past 30 years. Here, we apply consistent phylodynamic methods across multiple community-associated MRSA lineages to describe and contrast their patterns of emergence and dissemination. We...

Background Panton-Valentine leukocidin (PVL)-positive community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) are increasingly associated with infection outbreaks. Aim To investigate multiple suspected PVL-positive CA-MRSA outbreaks using whole-genome sequencing (WGS). Methods Forty-six suspected outbreak-associated isolates fr...

We investigated why a clinical meticillin-resistant Staphylococcus aureus (MRSA) isolate yielded false-negative results with some commercial PCR tests for MRSA detection. We found that an epidemic European CC1-MRSA-IV clone generally exhibits this behaviour. The failure of the assays was attributable to a large insertion in the orfX/SCCmec integrat...

Patients who carry nasal methicillin-resistant Staphylococcus aureus (MRSA) may also harbour MRSA in the oro-pharyngeal cavity. However, the naso-oro-pharyngeal co-carriage is infrequently assessed. The incidence of concurrent MRSA carriage of the naso-oro-pharynx was ascertained, and the sensitivity of two methods, a throat swab and a phosphate bu...

Background: A variety of rapid molecular PCR tests has been developed and commercialised that interrogate the junction site between the staphylococcal core genome, and the mobile genetic element (SCCmec) which harbours the gene responsible for methicillin-/beta-lactam-resistance. Aim: The purpose of the present study was to investigate why a clinic...

Background Linezolid is an antibiotic used to treat infections caused by multi-drug resistant Gram-positive bacteria. Linezolid resistance in enterococci has been reported with increasing frequency, with a recent rise in resistance encoded by optrA, poxtA or cfr. Aim To investigate a hospital outbreak of linezolid- and vancomycin-resistant Enteroc...

Patients with type 2 diabetes are at higher risk for periodontal disease and diabetic foot ulcer infections (DFUIs), the latter of which are predominantly caused by staphylococcal bacteria. Staphylococci have also been detected in the mouth, nose and gums (the oro-nasal cavity) of patients with periodontal disease and can move between the mouth and...

Objectives: To investigate the prevalence of the optrA, poxtA and cfr linezolid resistance genes in linezolid-resistant enterococci from Irish hospitals and to characterize associated plasmids. Methods: One hundred and fifty-four linezolid-resistant isolates recovered in 14 hospitals between June 2016 and August 2019 were screened for resistance...

Background Methicillin-susceptible Staphylococcus aureus (MSSA) bloodstream infection rates have risen steadily in recent years, with a marked decline in the corresponding rates due to methicillin-resistant S. aureus (MRSA). Screening for MSSA carriage is not routinely undertaken and MRSA screening is not universal, so the extent of S. aureus colon...

The drain openings of hand washbasins and sinks in hospitals represent a largely overlooked yet ubiquitous reservoir of microbial contamination that is increasingly recognized as a significant cause of patient infection, particularly with carbapenemase-producing Enterobacteriaceae. These bacteria have emerged relatively recently as a major health t...

The Bengal Bay clone (ST772) is a community-associated and multidrug-resistant Staphylococcus aureus lineage first isolated from Bangladesh and India in 2004. In this study, we showed that the Bengal Bay clone emerged from a virulent progenitor circulating on the Indian subcontinent. Its subsequent global transmission was associated with travel or...

Background: Hand washbasin U-bends have increasingly been associated with nosocomial outbreaks by Gram-negative bacteria, including Pseudomonas aeruginosa which is virtually ubiquitous in U-bends. Wastewater networks servicing U-bends are potential highways for trafficking pathogenic bacteria. Aim: To use P. aeruginosa to investigate trafficking...

The prevalence of methicillin-susceptible Staphylococcus aureus (MSSA) bloodstream infections (BSIs) has increased in many countries, including Ireland. This study aimed to investigate the molecular epidemiology of MSSA causing BSIs in Irish hospitals between 2006 and 2017, when MSSA BSIs increased, to identify any potential patient or pathogen con...

The evolution and global transmission of antimicrobial resistance has been well documented in Gram-negative bacteria and healthcare-associated epidemic pathogens, often emerging from regions with heavy antimicrobial use. However, the degree to which similar processes occur with Gram-positive bacteria in the community setting is less well understood...

This study investigated the recent emergence of multidrug-resistant Panton-Valentine leukocidin (PVL)-negative CC1-MRSA-IV in Ireland and Germany. Ten CC1-MSSA and 139 CC1-MRSA isolates recovered in Ireland between 2004 and 2017 were investigated. These were compared to 21 German CC1-MRSA, 10 Romanian CC1-MSSA, five Romanian CC1-MRSA and two UAE CC...

The arginine catabolic mobile element (ACME) was first described in methicillin-resistant Staphylococcus aureus and is considered to enhance transmission, persistence and survival. Subsequently ACMEs were shown to be more prevalent in the coagulase-negative Staphylococcus epidermidis. Previously, ACME types were distinguished by characteristic comb...

In recent years, approaches to tracking the spread of meticillin-resistant Staphylococcus aureus (MRSA) as part of outbreak management have used conventional DNA-based methods, including pulsed-field gel electrophoresis and spa typing. However, when a predominant clone is present, these methods may be insufficiently discriminatory. A literature sea...

Sequential methicillin-resistant Staphylococcus aureus (MRSA) isolates from patients following attempted mupirocin nasal decolonisation showed an increase in mupirocin resistance (MR) from 6.6% to 20%. MR isolates from patients who failed decolonization yielded indistinguishable spa types and carried multiple antimicrobial- and antiseptic-resistanc...

From 2009 to 2011 [transmission period (TP) 1] and 2014 to 2017 (TP2), two outbreaks involving community-associated clonal complex (CC) 88-MRSA spa types t186 and t786, respectively, occurred in the Neonatal Intensive Care Unit (NICU) of an Irish hospital (H1). This study investigated the relatedness of these isolates, their relationship to other C...

Staphylococcus aureus and Staphylococcus epidermidis are frequent commensals of the nares and skin and are considered transient oral residents. Reports on their prevalence in the oral cavity, periodontal pockets and subgingivally around infected oral implants are conflicting, largely due to methodological limitations. The prevalence of these specie...

ST239-MRSA-III is probably the oldest truly pandemic MRSA strain, circulating in many countries since the 1970s. It is still frequently isolated in some parts of the world although it has been replaced by other MRSA strains in, e.g., most of Europe. Previous genotyping work (Harris et al., 2010; Castillo-Ramírez et al., 2012) suggested a split in g...

Background: Diabetics are vulnerable to periodontal disease and diabetic foot ulcers (DFUs), the latter of which frequently become infected with staphylococci, predominantly Staphylococcus aureus. Our previous research revealed that Staphylococcus epidermidis is abundant in periodontal lesions, isolates of which frequently harbor the arginine catab...

Objective The aim of this study was to investigate co-located nasal Staphylococcus aureus and coagulase-negative staphylococci (CoNS) (mainly Staphylococcus epidermidis), recovered from healthy medical students in their preclinical year, prior to exposure to the healthcare environment, for the carriage of genes and genetic elements common to both s...

The arginine catabolic mobile element (ACME) was first described in the methicillin-resistant Staphylococcus aureus strain USA300 and is thought to facilitate survival on skin. To date three distinct ACME types have been characterized comprehensively in S. aureus and/or Staphylococcus epidermidis. Type I harbors the arc and opp3 operons encoding an...

Background: Outbreaks of infection associated with microbial biofilm in hospital hand washbasin U-bends are increasingly being reported. In a previous study the efficacy of a prototype automated U-bend decontamination method was demonstrated for a single non-hospital pattern washbasin. It used two electrochemically-activated solutions generated fr...

The USA300 North American epidemic (USA300-NAE) clone of methicillin-resistant Staphylococcus aureus has caused a wave of severe skin and soft tissue infections in the United States since it emerged in the early 2000s, but its geographic origin is obscure. Here we use the population genomic signatures expected from the serial founder effects of a g...

Mupirocin is used for eradicating methicillin-resistant S. aureus (MRSA) in nasal colonization. A plasmid-borne gene, mupA, is associated with high-level mupirocin resistance. Despite the fact that, among all MRSA from a tertiary care center in the German state of Saxony, the prevalence of mupA, encoding high-level mupirocin resistance, was approxi...

The type III arginine catabolic mobile element (ACME) was detected in three Staphylococcus epidermidis oral isolates recovered from separate patients (one healthy, one healthy with dental implants and one with periodontal disease) based on ACME- arc operon and - opp3 operon directed PCR. These isolates were subjected to whole genome sequencing to c...

Background: Linezolid is often the drug of last resort to treat infections caused by Gram-positive cocci. Linezolid resistance can be mutational (23S rRNA or L-protein) or, less commonly, acquired [predominantly cfr , conferring resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins and streptogramin A compounds (PhLOPS A ) or optrA...

Community-associated spa type t127/t922 methicillin-resistant Staphylococcus aureus (MRSA) prevalence increased from 1%-7% in Ireland between 2010–2015. This study tracked the spread of 89 such isolates from June 2013-June 2016. These included 78 healthcare-associated and 11 community associated-MRSA isolates from a prolonged hospital outbreak (H1)...

Pairwise SNV matrix of all 89 ST1-MRSA-IV isolates used to infer relatedness between isolates. (XLSX)

Pairwise SNV matrix—swab (B). Pairwise SNV matrix of 13 colonies from a single swab (from the same patient from which isolate M15/0221 was recovered) used to determine the maximum intra-host variation of an ST1-MRSA-IV isolate and inform interpretation of the ST1 pairwise SNV matrix. (XLSX)

Isolate information. Epidemiological, phenotypic and molecular characteristics of t127 and t922 methicillin-resistant Staphylococcus aureus isolates recovered from 17 hospitals, four other healthcare facilities and the community throughout Ireland between 2013 and 2016. (PDF)

Pairwise SNV matrix—swab (A). Pairwise SNV matrix of 13 colonies from a single swab (from the same patient from which isolate M13/0653 was recovered) used to determine the maximum intra-host variation of an ST1-MRSA-IV isolate and inform interpretation of the ST1 pairwise SNV matrix. (XLSX)

Patients with end-stage renal failure undergo regular haemodialysis (HD) and often develop episodes of Staphylococcus aureus bloodstream infection (BSI), which can re-occur. However, clinically, patients on HD, with S. aureus BSI, respond well to treatment, rarely developing overt signs of sepsis. We investigated the contributions of bacterial viru...

Staphylococcus aureus is a well-known colonizer and cause of infection among animals and it has been described from numerous domestic and wild animal species. The aim of the present study was to investigate the molecular epidemiology of S. aureus in a convenience sample of European wildlife and to review what previously has been observed in the sub...

Isolates, geographic origin, host species as well as full hybridization and typing data. (PDF)

Background: Washbasin U-bends are reservoirs of microbial contamination in healthcare environments. U-Bends are constantly full of water and harbour microbial biofilm. Aim: To develop an effective automated cleaning and disinfection system for U-bends using two solutions generated by electrochemical activation of brine including the disinfectant...

Ceftaroline is a new cephalosporin with activity against methicillin-resistant Staphylococcus aureus (MRSA). A collection of 17 clinical and veterinary mecC-positive MRSA isolates was tested to evaluate the in vitro efficacy of ceftaroline against recently emerged mecC-MRSA isolates. Minimum inhibitory concentrations (MICs) and minimum bactericidal...

Linezolid is often the drug of last resort for serious methicillin-resistant Staphylococcus aureus (MRSA) infections. Linezolid resistance is mediated by mutations in 23S rRNA and genes for ribosomal proteins, cfr encoding phenicol, lincosamide, oxazolidinone, pleuromutilin and streptogramin A (PhLOPSA) resistance, its homolgue cfr(B) or optrA conf...

Clonal complex (CC) 398 methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) are associated with carriage and infection among animals and humans but only a single case of CC398 MRSA has been reported in the Republic of Ireland (ROI). The present study investigated the molecular epidemiology of CC398 MRSA (...

Details of primers, thermal cycling conditions and positive control strains used in the present study. (PDF)

Whole-genome sequencing (WGS) of 41 patient and environmental ST22-MRSA-IV isolates recovered over six-weeks on one acute hospital ward in Dublin, Ireland, where ST22-MRSA IV is endemic, revealed 228 pairwise combinations differing by <40 single nucleotide variants corresponding to potential cross transmission events (CTEs). In contrast, 15 pairwis...

Background: Selective chromogenic media allowing one-step meticillin-resistant Staphylococcus aureus (MRSA) isolation and identification are widely used. However, the changing epidemiology of MRSA means that the suitability of these chromogenic media requires investigation. Aim: To evaluate the following chromogenic media - Colorex MRSA, MRSA Se...

This study compares the characteristics of Staphylococcus epidermidis (SE) and Staphylococcus haemolyticus (SH) isolates from epidemiologically unrelated infections in humans (Hu) (28 SE-Hu; 8 SH-Hu) and companion animals (CpA) (12 SE-CpA; 13 SH-CpA). All isolates underwent antimicrobial susceptibility testing, multilocus sequence typing and DNA mi...

Decontaminating dental chair unit (DCU) suction systems in a convenient, safe and effective manner is problematic. This study aimed to identify and quantify the extent of the problems using 25 DCUs, methodically eliminate these problems and develop an efficient approach for reliable, effective, automated disinfection. DCU suction system residual co...

Target genes, probes and primers. (PDF)

"nexus"-file used for the network graph based on concatenated MLST sequences (Figure 4). (NEX)

Overview of sequence types (STs), spa types, some characteristic genomic markers and fully sequenced genomes of the clonal complexes (CCs) described in this study (bold typeset indicates STs and spa types identified in the present study; italic typeset indicates STs found by the authors in MSSA isolates or spa types described in literature or publi...

Complete hybridisation results for MRSA strains examined in this study. (PDF)

"nexus"-file used for the network graph based on hybridisation profiles (Figure 5). (NEX)

Full array hybridisation and PCR results of the hedgehog isolates from this study and, for comparison, of CC130-MRSA-XI isolates from [7]. (PDF)