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Antimicrobial resistance (AMR) is considered a global threat, and novel drug discovery needs to be complemented with systematic and standardized epidemiological surveillance. Surveillance data are currently generated using phenotypic characterization. However, due to poor scalability, this approach does little for true epidemiological investigations. There is a strong case for whole-genome sequencing (WGS) to enhance the phenotypic data. To establish global AMR surveillance using WGS, we developed a laboratory implementation approach that we applied within the NIHR Global Health Research Unit (GHRU) on Genomic Surveillance of Antimicrobial Resistance. In this paper, we outline the laboratory implementation at 4 units: Colombia, India, Nigeria, and the Philippines. The journey to embedding WGS capacity was split into 4 phases: Assessment, Assembly, Optimization, and Reassessment. We show that on-boarding WGS capabilities can greatly enhance the real-time processing power within regional and national AMR surveillance initiatives, despite the high initial investment in laboratory infrastructure and maintenance. Countries looking to introduce WGS as a surveillance tool could begin by sequencing select Global Antimicrobial Resistance Surveillance System (GLASS) priority pathogens that can demonstrate the standardization and impact genome sequencing has in tackling AMR.

Antimicrobial resistance (AMR) is a major global health challenge, especially in low- and middle-income countries (LMIC). Programs that appropriate antibiotic use such as antimicrobial stewardship, is a global health strategy adopted by the World Health Organization to contain threats posed by AMR. Unfortunately, many LMICs are at best left behind in the process of developing antimicrobial stewardship programs (ASP). We highlighted the roles of the clinical microbiology laboratory in antimicrobial stewardship and challenges associated with the program in LMICs. We further suggested ways forward in the adoption and implementation of existing programs in resource-limited settings. There is generally nonexistent or at best, fewer ASP in the LMICs. More efforts need to be channeled toward fighting the AMR scourge, primarily by adopting ASP while utilizing the little resources available.

Objectives This study describes the clinical features and outcomes of patients with bloodstream infection (BSI) due to Enterococcus spp. and identified factors predictive of mortality. Methods This analysis is part of a prospective multicentre observational study of consecutive hospitalised patients with BSI conducted from March 2012 to December 2012 in 31 internal medicine wards in Italy. Patients with enterococcal BSI were selected from the entire cohort. Patient characteristics, therapeutic interventions and outcome were reviewed. Cox regression analysis was performed to identify factors associated with in-hospital mortality. Hazard ratios (HRs) and 95% interval confidences (CIs) were calculated. Results Among 533 patients with BSI, 41 (7.7%) had BSI by Enterococcus spp. (28 Enterococcus faecalis, 4 Enterococcus faecium and 3 each of Enterococcus avium, Enterococcus casseliflavus and Enterococcus gallinarum). Six BSIs (14.6%) were polymicrobial. Median (IQR) patient age was 73 (66–85.5) years. In-hospital mortality was 24.4%. Polymicrobial infection (HR = 9.100, 95% CI 1.295–63.949; P = 0.026), age (HR = 1.261, 95% CI 1.029–1.546; P = 0.025) and SOFA score (HR = 1.244, 95% CI 1.051–1.474; P = 0.011) were risk factors for in-hospital mortality. Conversely, receiving an alert from the microbiology laboratory before obtaining final antimicrobial susceptibility results was associated with survival (HR = 0.073, 95% CI 0.007–0.805; P = 0.033). Conclusion BSI due to Enterococcus spp. in elderly patients is associated with high mortality. Polymicrobial infection, age and SOFA score are factors associated with poor outcome. Conversely, early alert from the microbiology laboratory improves patient survival.

Single-use plastics have often replaced more sustainable materials in microbiology laboratories. Keeping in mind that one of the objectives of the United Nations Sustainable Development Goals is responsible consumption and production, we wanted to document how many single-use plastic items could be saved by taking reduction and reuse approaches in a microbiology laboratory. After taking 4 weeks to document the baseline levels of single-use plastic waste being generated in our laboratory and identifying ways to reduce our reliance on them, we implemented various reduction and reuse approaches and then documented our plastic use over a 7-week period. Reduction approaches included moving to sustainable materials, such as reusable wooden sticks for patch plating and metal loops for inoculation. Reuse approaches focused on reusing plastic tubes via a chemical decontamination station and autoclaving, facilitating the reduction of single-use plastics and a decrease in the amount of waste generated. By utilizing reduction and reuse strategies, which could be implemented in other microbiology laboratories, substantial single-use plastic savings were achieved. These savings had an impact on the amount of biohazard waste being autoclaved and incinerated, as well as generating substantial cost savings for the research institute. The reductions in waste documented in this study could act as a benchmark for others wanting to implement the changes described.

Clinical microbiologists and microbiology laboratories are experiencing changes due to evolving views on ‘healthcare delivery’ as an economic activity, due to changes in the medical environment and the demographics of the workforce, and technical evolution. Cost-effectiveness of laboratory procedures has been achieved through consolidation and integration of laboratories. Consolidation offers economy of scale and reduction in numbers of on-site staff, but also leads to separation of microbiologists from their clinical colleagues. Integration puts different laboratory disciplines under a single management, and leads to reorganisation of laboratories along common work-lines. Cost-savings combined with on-site availability of laboratories are achieved at the expense of a reduction in the influence of microbiologists in the daily running of the laboratory. Medically, there is growing emphasis on evidence-based diagnostics. Because of time-delays inherent in culturing, microbiology has a limited impact on patient outcomes. Increased clinical relevance of microbiological testing through rapid testing is mandatory. There is an increasing shortage in Europe and the USA of trained microbiology laboratory technicians and microbiologists. This reinforces the trend towards more automation and integration. Technological advances, particularly in molecular diagnostics, offer the possibility of rapid reporting and improvement of the impact of clinical microbiology on patient management. Molecular tests, however, fit perfectly the concept of an integrated laboratory and may further loosen the link between microbiologist and microbiology tests. The challenge for clinical microbiology will be to use new techniques to improve its cost-effectiveness and impact on infectious disease management. The future organisation of microbiology laboratories must support this but is itself of secondary importance. The training of future microbiologists must prepare them for this changing environment.

Background: It is expected that health information technology (HIT) will deliver a safer, more efficient and effective health care system. The aim of this study was to undertake a qualitative and video-ethnographic examination of the impact of information technologies on work processes in the reception area of a Microbiology Department, to ascertain what changed, how it changed and the impact of the change. Materials and Methods: The setting for this study was the microbiology laboratory of a large tertiary hospital in Sydney. The study consisted of qualitative (interview and focus group) data and observation sessions for the period August 2005 to October 2006 along with video footage shot in three sessions covering the original system and the two stages of the Cerner implementation. Data analysis was assisted by NVivo software and process maps were produced from the video footage. Results: There were two laboratory information systems observed in the video footage with computerized provider order entry introduced four months later. Process maps highlighted the large number of pre data entry steps with the original system whilst the newer system incorporated many of these steps in to the data entry stage. However, any time saved with the new system was offset by the requirement to complete some data entry of patient information not previously required. Other changes noted included the change of responsibilities for the reception staff and the physical changes required to accommodate the increased activity around the data entry area. Conclusions: Implementing a new HIT is always an exciting time for any environment but ensuring that the implementation goes smoothly and with minimal trouble requires the administrator and their team to plan well in advance for staff training, physical layout and possible staff resource reallocation.

Objective To analyse the quality of ordering, collection and transport of specimens for microbiological analysis by a department of orthopedic surgery. Methods The analysis consisted of a prospective formal evaluation performed by two consultant microbiologists. Results One hundred and seventeen consecutive requests were audited. These requests belonged to 55 clinical episodes, 39 of which were of (presumed) infection and 16 of surveillance. The main sites sampled were: joint 28 (51%), and extra-articular bone or tissue 6 (11%). Of 98 surgical specimens, 20 (20%) yielded a relevant microorganism. The requests were classified as definitely appropriate in 67% and 85% of episodes, by the two consultants respectively. No request was considered unjustified. Collection, handling and transport were categorized as definitely appropriate in 56% and 73% of requests. Analysis of compliance with an existing protocol for prosthetic joint revision revealed similar errors. Conclusion Audits of this type can give invaluable information about the area of uncertainty between the clinician and the laboratory and can identify appropriate measures for corrective action.