John E. Coia

Emergence and global spread of epidemic healthcare-associated Clostridium difficile

Epidemic C. difficile (027/BI/NAP1) has rapidly emerged in the past decade as the leading cause of antibiotic-associated diarrhea worldwide. However, the key events in evolutionary history leading to its emergence and the subsequent patterns of global spread remain unknown. Here, we define the global population structure of C. difficile 027/BI/NAP1 using whole-genome sequencing and phylogenetic analysis. We show that two distinct epidemic lineages, FQR1 and FQR2, not one as previously thought, emerged in North America within a relatively short period after acquiring the same fluoroquinolone resistance–conferring mutation and a highly related conjugative transposon. The two epidemic lineages showed distinct patterns of global spread, and the FQR2 lineage spread more widely, leading to healthcare-associated outbreaks in the UK, continental Europe and Australia. Our analysis identifies key genetic changes linked to the rapid transcontinental dissemination of epidemic C. difficile 027/BI/NAP1 and highlights the routes by which it spreads through the global healthcare system.

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe.

Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery, spreading efficiently via low-dose fecal-oral transmission. Historically, S. sonnei has been predominantly responsible for dysentery in developed countries but is now emerging as a problem in the developing world, seeming to replace the more diverse Shigella flexneri in areas undergoing economic development and improvements in water quality. Classical approaches have shown that S. sonnei is genetically conserved and clonal. We report here whole-genome sequencing of 132 globally distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and that diversified into several distinct lineages with unique characteristics. Our analysis suggests that the majority of this diversification occurred in Europe and was followed by more recent establishment of local pathogen populations on other continents, predominantly due to the pandemic spread of a single, rapidly evolving, multidrug-resistant lineage.

Packed with Salmonella--investigation of an international outbreak of Salmonella Senftenberg infection linked to contamination of prepacked basil in 2007.

Salmonella Senftenberg is uncommon in the United Kingdom. In January-June 2007, the Health Protection Agency reported on 55 primary human cases of Salmonella Senftenberg in England and Wales. In May 2007, fresh basil sold in the United Kingdom was found to be contaminated with Salmonella Senftenberg. We launched an investigation to elucidate the cause of this outbreak. Isolates were examined using plasmid profiling and pulsed-field gel electrophoresis, and the outbreak strain (SSFTXB.0014) was identified. We enquired via Enter-net whether other countries had isolated the outbreak strain, analyzed samples of fresh herbs from U.K. retailers, and interviewed patients on food history. Thirty-two patient-cases were referred to this outbreak in England and Wales. Onsets of illness occurred between 5 March and 6 June 2007. Fifty-six percent of patient-cases were females and 90% adults (>20 years old); three were admitted to hospital as a result of Salmonella infection. Scotland, Denmark, the Netherlands, and the United States reported on 19 cases of Salmonella Senftenberg infection presenting with the outbreak strain since January 2007. Eight samples of prepacked fresh basil imported from Israel tested positive with the same strain. A minority of patients could recall the consumption of basil before illness, and some reported consumption of products where basil was a likely ingredient. Environmental investigations in Israel did not identify the contamination source. Microbiological evidence suggested an association between contamination of fresh basil and the cases of Salmonella Senftenberg infection, leading to withdrawal of basil from all potentially affected batches from the U.K. market.

An ecological approach to assessing the epidemiology of antimicrobial resistance in animal and human populations

We examined long-term surveillance data on antimicrobial resistance (AMR) in Salmonella Typhimurium DT104 (DT104) isolates from concurrently sampled and sympatric human and animal populations in Scotland. Using novel ecological and epidemiological approaches to examine diversity, and phenotypic and temporal relatedness of the resistance profiles, we assessed the more probable source of resistance of these two populations. The ecological diversity of AMR phenotypes was significantly greater in human isolates than in animal isolates, at the resolution of both sample and population. Of 5200 isolates, there were 65 resistance phenotypes, 13 unique to animals, 30 unique to humans and 22 were common to both. Of these 22, 11 were identified first in the human isolates, whereas only five were identified first in the animal isolates. We conclude that, while ecologically connected, animals and humans have distinguishable DT104 communities, differing in prevalence, linkage and diversity. Furthermore, we infer that the sympatric animal population is unlikely to be the major source of resistance diversity for humans. This suggests that current policy emphasis on restricting antimicrobial use in domestic animals may be overly simplistic. While these conclusions pertain to DT104 in Scotland, this approach could be applied to AMR in other bacteria–host ecosystems.

Clinical studies of the High-Intensity Narrow-Spectrum light Environmental Decontamination System (HINS-light EDS), for continuous disinfection in the burn unit inpatient and outpatient settings §

Infections are the leading cause of morbidity and mortality in burn patients and prevention of contamination from exogenous sources including the hospital environment is becoming increasingly emphasised. The High-Intensity Narrow-Spectrum light Environmental Decontamination System (HINS-light EDS) is bactericidal yet safe for humans, allowing continuous disinfection of the environment surrounding burn patients. Environmental samples were collected from inpatient isolation rooms and the outpatient clinic in the burn unit, and comparisons were then made between the bacterial contamination levels observed with and without use of the HINS-light EDS. Over 1000 samples were taken. Inpatient studies, with sampling carried out at 0800 h, demonstrated a significant reduction in the average number of bacterial colonies following HINS-light EDS use of between 27% and 75%, (p<0.05). There was more variation when samples were taken at times of increased activity in the room. Outpatient studies during clinics demonstrated a 61% efficacy in the reduction of bacterial contamination on surfaces throughout the room during the course of a clinic (p=0.02). The results demonstrate that use of the HINS-light EDS allows efficacious bacterial reductions over and above that achieved by standard cleaning and infection control measures in both inpatient and outpatient settings in the burn unit.

Environmental risk factors for sporadic Escherichia coli O157 infection in Scotland: Results of a descriptive epidemiology study

The objective of the study was to obtain detailed descriptive epidemiological information on sporadic verocytotoxin-producing Escherichia coli O157 infection in Scotland in relation to transmission routes and host-related risk factors. Using a standardized questionnaire, the study was carried out throughout Scotland over an 18-month period from July 1992 and co-ordinated at the Communicable Diseases and Environmental Health (Scotland) Unit, Glasgow (CDEH(S)U). The subjects were laboratory-confirmed cases of Escherichia coli O157 infection, of whom 138 met the criteria for inclusion in the study. The most important findings were the high proportion of cases who had been exposed to environmental factors such as farm animals and/or their by-products; or who had participated in gardening or garden-play; or who had suspected or confirmed household water supply problems, prior to the onset of illness. The frequency and relative importance of environmental risk factors requires further quantification and study in order to assess where control measures can be directed most effectively. The implications for the NHS in preventing this crippling, life-threatening infection are considerable, not least in relation to hospitalization, dialysis and renal transplantation costs.

Guidance on the use of respiratory and facial protection equipment

Summary Infectious micro-organisms may be transmitted by a variety of routes, and some may be spread by more than one route. Respiratory and facial protection is required for those organisms that are usually transmitted via the droplet/airborne route, or when airborne particles have been artificially created, such as during ‘aerosol-generating procedures’. A range of personal protective equipment that provides different degrees of facial and respiratory protection is available. It is apparent from the recent experiences with severe acute respiratory syndrome and pandemic (H1N1) 2009 influenza that healthcare workers may have difficulty in choosing the correct type of facial and respiratory protection in any given clinical situation. To address this issue, the Scientific Development Committee of the Healthcare Infection Society established a short-life working group to develop guidance. The guidance is based upon a review of the literature, which is published separately, and expert consensus.

Gram-negative bacteraemia in haemodialysis

BACKGROUND Patients on renal replacement therapy experience higher rates of morbidity and mortality, infection being the second commonest cause of death. In our haemodialysis population, we identify the pathogens, sensitivity patterns, sources of infection and outcomes of Gram-negative bacteraemia. METHODS Data from the NHS Greater Glasgow & Clyde and NHS Forth Valley haemodialysis population were collected July 2011 to April 2014 through an interrogation of the renal unit electronic patient record, and confirmed by an independent search of the Microbiology database. RESULTS Over 544 377 haemodialysis days, 84 patients experienced 95 Gram-negative bacteraemia events, a rate of 0.175 events per 1000 haemodialysis days, which varied with dialysis modality: non-tunnelled central venous catheters 4.77, arteriovenous grafts 0.24, tunnelled central venous catheters 0.21, and arteriovenous fistulae 0.11 per 1000 haemodialysis days. The commonest sources of bacteraemia were central venous catheters (CVCs) (16.8%, n = 16), infected ulcers (14.7%, n = 14), urinary (10.5%, n = 10), biliary (9.5%, n = 9) and intra-abdominal (9.5%, n = 9).The principal organisms were Escherichia coli (49.5%, n = 47), Enterobacter spp. (13.1%, n = 13), Klebsiella spp. (11.1%, n = 11), Proteus mirabilis (6.1%, n = 6) and Pseudomonas aeruginosa (5.1%, n = 5). Of the Enterobacteriaceae (n = 84), 88% were sensitive to gentamicin, 81% to ciprofloxacin, 91% to piperacillin-tazobactam and 100% were sensitive to meropenem.Three-month case mortality was 25.3% (n = 24). Ten patients (11.9%) had more than one Gram-negative bacteraemia; of these, nine patients (90.0%) were the same causative organism, predominantly E. coli. CONCLUSIONS CVCs and diabetic foot ulcers remain significant risk factors for Gram-negative bacteraemia, highlighting the importance of vascular access planning. Despite good levels of antibiotic sensitivity, the early mortality following Gram-negative bacteraemia remains high, supporting aggressive treatment of such pathogens.

Continuous decontamination of an intensive care isolation room during patient occupancy using 405 nm light technology

Environmental contamination within intensive care units (ICU) is recognised as a source of patient infection, and improved cleaning and disinfection methods are continually being sought. Visible light of 405 nm has been shown to have bactericidal properties, and this communication reports on the use of a ceiling-mounted 405 nm light system for continuous environmental disinfection of contact surfaces and air in an occupied ICU isolation room. Levels of bacterial contamination on a range of contact surfaces around the room were assessed before, during and after use of the system. For each study, the lighting units were operated continuously during daylight hours. Results demonstrate that the spatial distribution of bacterial contamination was reduced almost uniformly across all sampled contact surfaces during use of the 405 nm light system. Pooled data showed that significant reductions in overall bacterial contamination around the room were achieved, with bacterial counts reduced by up to 67% (p=0.0001) over and above that achieved with standard cleaning and infection control procedures alone. Use of 405 nm light significantly reduced environmental contamination across almost all sampled contact surfaces within the ICU isolation room. This has particular benefit in ICU where equipment and other ‘hand-touch’ sites make routine cleaning difficult, thus helping maintain a cleaner environment, and contributing to reducing cross-infection from environmental sources.

Respiratory and facial protection: a critical review of recent literature

Summary Infectious micro-organisms may be transmitted by a variety of routes. This is dependent on the particular pathogen and includes bloodborne, droplet, airborne, and contact transmission. Some micro-organisms are spread by more than one route. Respiratory and facial protection is required for those organisms which are usually transmitted via the droplet and/or airborne routes or when airborne particles have been created during ‘aerosol-generating procedures’. This article presents a critical review of the recently published literature in this area that was undertaken by Health Protection Scotland and the Healthcare Infection Society and which informed the development of guidance on the use of respiratory and facial protection equipment by healthcare workers.