What\u27s in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015

Technological advancements in fields such as molecular genetics and the human microbiome have resulted in an unprecedented recognition of new bacterial genus/species designations by the International Journal of Systematic and Evolutionary Microbiology. Knowledge of designations involving clinically significant bacterial species would benefit clinical microbiologists in the context of emerging pathogens, performance of accurate organism identification, and antimicrobial susceptibility testing. In anticipation of subsequent taxonomic changes being compiled by the Journal of Clinical Microbiology on a biannual basis, this compendium summarizes novel species and taxonomic revisions specific to bacteria derived from human clinical specimens from the calendar years 2012 through 2015

Correction for Munson and Carroll, “What’s in a Name? New Bacterial Species and Changes to Taxonomic Status from 2012 through 2015”

Author Correction

Diagnosis of Clostridium difficile infection: An ongoing conundrum for clinicians and for clinical laboratories

SUMMARY: Clostridium difficile is a formidable nosocomial and community-acquired pathogen, causing clinical presentations ranging from asymptomatic colonization to self-limiting diarrhea to toxic megacolon and fulminant colitis. Since the early 2000s, the incidence of C. difficile disease has increased dramatically, and this is thought to be due to the emergence of new strain types. For many years, the mainstay of C. difficile disease diagnosis was enzyme immunoassays for detection of the C. difficile toxin(s), although it is now generally accepted that these assays lack sensitivity. A number of molecular assays are commercially available for the detection of C. difficile. This review covers the history and biology of C. difficile and provides an in-depth discussion of the laboratory methods used for the diagnosis of C. difficile infection (CDI). In addition, strain typing methods for C. difficile and the evolving epidemiology of colonization and infection with this organism are discussed. Finally, considerations for diagnosing C. difficile disease in special patient populations, such as children, oncology patients, transplant patients, and patients with inflammatory bowel disease, are described. As detection of C. difficile in clinical specimens does not always equate with disease, the diagnosis of C. difficile infection continues to be a challenge for both laboratories and clinicians

Non-linear temperature response of Bragg gratings in doped and un-doped holey polymer optical fibre

We present measurements on the non-linear temperature response of fibre Bragg gratings recorded in pure and trans-4-stilbenemethanol-doped polymethyl methacrylate (PMMA) holey fibres

Perceptions and Practices of Key Worker Stakeholder Groups in Hospital Animal- Assisted Intervention Programs on Occupational Benefits and Perceived Risks

Background: Animal-assisted intervention (AAI) programs, used widely for patient benefit, have increasingly been used for healthcare workers (HCW) to reduce occupational stress. However, there are barriers to these programs which limit their utilization, for both patients and HCW, specifically infectious disease concerns. The aim of the research project is to identify barriers and facilitators to AAI program use for healthcare worker benefit, and determine knowledge, beliefs, and practices regarding infectious disease risk and control policies, in order to understand the contextual parameters of program implementation. Methods: We collected perceptions of key stakeholders involved with hospital AAI programs (HCW and AAI workers) through semi-structured in-depth interviews. We used framework analysis to guide thematic coding, completed independently by three researchers. Results: We interviewed 37 participants in this study. We divided our themes into two topic areas: program use for HCW and perceived infectious disease risk. Use for healthcare workers included perspectives on the benefits for HCW and program barriers and facilitators (specifically collaboration and leadership). Perceived risk included opinions on infection concerns with AAI, thoughts on control measures to reduce this risk, and responsibility for safety during these programs. Conclusions: While significant benefits were reported for HCW, they were limited by administrative barriers and hazard concerns. Facilitators to surmount these barriers are best implemented with collaboration across the hospital and appropriate leadership roles to direct safe program implementation. By addressing these barriers through targeted facilitators in the form of evidence-backed guidelines, AAI programs can be used to benefit both patients and HCW

Multidrug-resistant and methicillin-resistant Staphylococcus aureus (MRSA) in hog slaughter and processing plant workers and their community in North Carolina (USA)

Background: Use of antimicrobials in industrial food-animal production is associated with the presence of antimicrobial resistant Staphylococcus aureus among animals and humans. Hog slaughter/processing plants process large numbers of animals from industrial animal operations, and are environments conducive to the exchange of bacteria between animals and workers. Objectives: To compare the prevalence of methicillin-resistant S. aureus (MRSA) and multidrug resistant S. aureus(MDRSA) carriage between processing plant workers, their household members, and community residents. Methods: We conducted a cross-sectional study of hog slaughter/processing plant workers, their household members, and community residents in North Carolina. Participants responded to a questionnaire and provided a nasal swab. Swabs were tested for S. aureus, and isolates tested for antimicrobial susceptibility and subjected to multilocus sequence typing. Results: The prevalence of S. aureus was 21.6%, 30.2%, and 22.5% among 162 workers, 63 household members, and 111 community residents, respectively. The overall prevalence of MRSA and MDRSA tested by disk diffusion was 4.8% and 6.9%, respectively. The adjusted prevalence of MDRSA among workers was 1.96 times (95% CI: 0.71, 5.45) the prevalence in community residents. The adjusted average number of antimicrobial classes to which S. aureus isolates from workers were resistant was 2.54 times (95% CI: 1.16, 5.56) the number among isolates from community residents. One MRSA isolate and two MDRSA isolates from workers were identified as sequence type 398, a type associated with exposure to livestock. Conclusions: Although the prevalence of S. aureus and MRSA was similar in hog slaughter/processing plant workers and their household and community members, S. aureus isolates from workers were resistant to a greater number of antimicrobial classes. These findings may be related to the non-therapeutic use of antimicrobials in food-animal production

Reflections on the Cost of Low-Cost Whole Genome Sequencing: Framing the Health Policy Debate

The cost of whole genome sequencing is dropping rapidly. There has been a great deal of enthusiasm about the potential for this technological advance to transform clinical care. Given the interest and significant investment in genomics, this seems an ideal time to consider what the evidence tells us about potential benefits and harms, particularly in the context of health care policy. The scale and pace of adoption of this powerful new technology should be driven by clinical need, clinical evidence, and a commitment to put patients at the centre of health care policy

‘Trying to pin down jelly’ - exploring intuitive processes in quality assessment for meta-ethnography

Background: Studies that systematically search for and synthesise qualitative research are becoming more evident in health care, and they can make an important contribution to patient care. However, there is still no agreement as to whether, or how we should appraise studies for inclusion. We aimed to explore the intuitive processes that determined the ‘quality’ of qualitative research for inclusion in qualitative research syntheses. We were particularly interested to explore the way that knowledge was constructed. Methods: We used qualitative methods to explore the process of quality appraisal within a team of seven qualitative researchers funded to undertake a meta-ethnography of chronic non-malignant musculoskeletal pain. Team discussions took place monthly between October 2010 and June 2012 and were recorded and transcribed. Data was coded and organised using constant comparative method. The development of our conceptual analysis was both iterative and collaborative. The strength of this team approach to quality came from open and honest discussion, where team members felt free to agree, disagree, or change their position within the safety of the group. Results: We suggest two core facets of quality for inclusion in meta-ethnography - (1) Conceptual clarity; how clearly has the author articulated a concept that facilitates theoretical insight. (2) Interpretive rigour; fundamentally, can the interpretation ‘be trusted?’ Our findings showed that three important categories help the reader to judge interpretive rigour: (ii) What is the context of the interpretation? (ii) How inductive is the interpretation? (iii) Has the researcher challenged their interpretation? Conclusions: We highlight that methods alone do not determine the quality of research for inclusion into a meta-ethnography. The strength of a concept and its capacity to facilitate theoretical insight is integral to meta-ethnography, and arguably to the quality of research. However, we suggest that to be judged ‘good enough’ there also needs to be some assurance that qualitative findings are more than simply anecdotal. Although our conceptual model was developed specifically for meta-ethnography, it may be transferable to other research methodologies