bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonselective Persistence of a Rickettsia conorii Extrachromosomal Plasmid during Mammalian Infection
Authors: Riley Sean P. , Fish Abigail I. , Garza Daniel A. , Banajee Kaikhushroo H. , Harris Emma K. , del Piero Fabio , Martinez Juan J. 
Published: January 2016

ABSTRACT

Scientific analysis of the genus
Rickettsia
is undergoing a rapid period of change with the emergence of viable genetic tools. The development of these tools for the mutagenesis of pathogenic bacteria will permit forward genetic analysis of
Rickettsia
pathogenesis. Despite these advances, uncertainty still remains regarding the use of plasmids to study these bacteria in
in vivo
mammalian models of infection, namely, the potential for virulence changes associated with the presence of extrachromosomal DNA and nonselective persistence of plasmids in mammalian models of infection. Here, we describe the transformation of
Rickettsia conorii
Malish 7 with the plasmid pRam18dRGA[AmTrCh]. Transformed
R. conorii
stably maintains this plasmid in infected cell cultures, expresses the encoded fluorescent proteins, and exhibits growth kinetics in cell culture similar to those of nontransformed
R. conorii
. Using a well-established murine model of fatal Mediterranean spotted fever, we demonstrate that
R. conorii
(pRam18dRGA[AmTrCh]) elicits the same fatal outcomes in animals as its untransformed counterpart and, importantly, maintains the plasmid throughout infection in the absence of selective antibiotic pressure. Interestingly, plasmid-transformed
R. conorii
was readily observed both in endothelial cells and within circulating leukocytes. Together, our data demonstrate that the presence of an extrachromosomal DNA element in a pathogenic rickettsial species does not affect either
in vitro
proliferation or
in vivo
infectivity in models of disease and that plasmids such as pRam18dRGA[AmTrCh] are valuable tools for the further genetic manipulation of pathogenic rickettsiae.
Intestinal Epithelial Toll-Like Receptor 4 Signaling Affects Epithelial Function and Colonic Microbiota and Promotes a Risk for Transmissible Colitis
Authors: Dheer Rishu , Santaolalla Rebeca , Davies Julie M. , Lang Jessica K. , Phillips Matthew C. , Pastorini Cristhine , Vazquez-Pertejo Maria T. , Abreu Maria T. 
Published: January 2016

ABSTRACT
Evidence obtained from gene knockout studies supports the role of Toll-like receptor 4 (TLR4) in intestinal inflammation and microbiota recognition. Increased epithelial TLR4 expression is observed in patients with inflammatory bowel disease. However, little is known of the effect of increased TLR4 signaling on intestinal homeostasis. Here, we examined the effect of increased TLR4 signaling on epithelial function and microbiota by using transgenic villin-TLR4 mice that overexpress TLR4 in the intestinal epithelium. Our results revealed that villin-TLR4 mice are characterized by increases in the density of mucosa-associated bacteria and bacterial translocation. Furthermore, increased epithelial TLR4 signaling was associated with an impaired epithelial barrier, altered expression of antimicrobial peptide genes, and altered epithelial cell differentiation. The composition of the colonic luminal and mucosa-associated microbiota differed between villin-TLR4 and wild-type (WT) littermates. Interestingly, WT mice cohoused with villin-TLR4 mice displayed greater susceptibility to acute colitis than singly housed WT mice did. The results of this study suggest that epithelial TLR4 expression shapes the microbiota and affects the functional properties of the epithelium. The changes in the microbiota induced by increased epithelial TLR4 signaling are transmissible and exacerbate dextran sodium sulfate-induced colitis. Together, our findings imply that host innate immune signaling can modulate intestinal bacteria and ultimately the host's susceptibility to colitis.
Succinic Semialdehyde Promotes Prosurvival Capability of Agrobacterium tumefaciens
Authors: Wang Chao , Tang Desong , Gao Yong-Gui , Zhang Lian-Hui 
Published: January 2016

ABSTRACT

Succinic semialdehyde (SSA), an important metabolite of γ-aminobutyric acid (GABA), is a ligand of the repressor AttJ regulating the expression of the
attJ-attKLM
gene cluster in the plant pathogen
Agrobacterium tumefaciens
. While the response of
A. tumefaciens
to GABA and the function of
attKLM
have been extensively studied, genetic and physiological responses of
A. tumefaciens
to SSA remain unknown. In combination with microarray and genetic approaches, this study sets out to explore new roles of the SSA-AttJKLM regulatory mechanism during bacterial infection. The results showed that SSA plays a key role in regulation of several bacterial activities, including C
4
-dicarboxylate utilization, nitrate assimilation, and resistance to oxidative stress. Interestingly, while the SSA relies heavily on the functional AttKLM in mediating nitrate assimilation and oxidative stress resistance, the compound could regulate utilization of C
4
-dicarboxylates independent of AttJKLM. We further provide evidence that SSA controls C
4
-dicarboxylate utilization through induction of an SSA importer and that disruption of
attKLM
attenuates the tumorigenicity of
A. tumefaciens
. Taken together, these findings indicate that SSA could be a potent plant signal which, together with AttKLM, plays a vital role in promoting the bacterial prosurvival abilities during infection.

IMPORTANCE
Agrobacterium tumefaciens
is a plant pathogen causing crown gall diseases and has been well known as a powerful tool for plant genetic engineering. During the long history of microbe-host interaction,
A. tumefaciens
has evolved the capabilities of recognition and response to plant-derived chemical metabolites. Succinic semialdehyde (SSA) is one such metabolite. Previous results have demonstrated that SSA functions to activate a quorum-quenching mechanism and thus to decrease the level of quorum-sensing signals, thereby avoiding the elicitation of a plant defense. Here, we studied the effect of SSA on gene expression at a genome-wide level and reported that SSA also promotes bacterial survival during infection. These findings provide a new insight on the biological significance of chemical signaling between agrobacteria and plant hosts.
Inositol-Requiring Enzyme 1-Dependent Activation of AMPK Promotes Brucella abortus Intracellular Growth
Authors: Liu Ning , Li Yingying , Dong Chunyan , Xu Xiaohan , Wei Pan , Sun Wanchun , Peng Qisheng 
Published: January 2016

ABSTRACT

AMP-activated protein kinase (AMPK) is a serine/threonine kinase that is well conserved during evolution. AMPK activation inhibits production of reactive oxygen species (ROS) in cells via suppression of NADPH oxidase. However, the role of AMPK during the process of
Brucella
infection remains unknown. Our data demonstrate that
B. abortus
infection induces AMPK activation in HeLa cells in a time-dependent manner. The known AMPK kinases LKB1, CAMKKβ, and TAK1 are not required for the activation of AMPK by
B. abortus
infection. Instead, this activation is dependent on the RNase activity of inositol-requiring enzyme 1 (IRE1). Moreover, we also found that
B. abortus
infection-induced IRE1-dependent activation of AMPK promotes
B. abortus
intracellular growth with peritoneal macrophages via suppression of NADPH-derived ROS production.

IMPORTANCE
Previous studies showed that
B. abortus
infection does not promote any oxidative burst regulated by NADPH oxidase. However, the underlying mechanism remains elusive. We report for the first time that AMPK activation caused by
B. abortus
infection plays important role in NADPH oxidase-derived ROS production.
Impact of Different Target Sequences on Type III CRISPR-Cas Immunity
Authors: Maniv Inbal , Jiang Wenyan , Bikard David , Marraffini Luciano A. 
Published: January 2016

ABSTRACT

Clustered regularly interspaced short palindromic repeat (CRISPR) loci encode an adaptive immune system of prokaryotes. Within these loci, sequences intercalated between repeats known as “spacers” specify the targets of CRISPR immunity. The majority of spacers match sequences present in phages and plasmids; however, it is not known whether there are differences in the immunity provided against these diverse invaders. We studied this issue using the
Staphylococcus epidermidis
CRISPR system, which harbors spacers matching both phages and plasmids. We determined that this CRISPR system provides similar levels of defense against the conjugative plasmid pG0400 and the bacteriophage CNPX. However, whereas antiplasmid immunity was very sensitive to the introduction of mismatches in the target sequence, mutations in the phage target were largely tolerated. Placing the phage and plasmid targets into a vector that can be both conjugated and transduced, we demonstrated that the route of entry of the target has no impact on the effect of the mismatches on immunity. Instead, we established that the specific sequences of each spacer/target determine the susceptibility of the
S. epidermidis
CRISPR system to mutations. Therefore, spacers that are more resistant to mismatches would provide long-term immunity against phages and plasmids that otherwise would escape CRISPR targeting through the accumulation of mutations in the target sequence. These results uncover an unexpected complexity in the arms race between CRISPR-Cas systems and prokaryotic infectious genetic elements.

IMPORTANCE
CRISPR-Cas loci protect bacteria and archaea from both phage infection and plasmid invasion. These loci harbor short sequences of phage and plasmid origin known as “spacers” that specify the targets of CRISPR-Cas immunity. The presence of a spacer sequence matching a phage or plasmid ensures host immunity against infection by these genetic elements. In turn, phages and plasmids constantly mutate their targets to avoid recognition by the spacers of the CRISPR-Cas immune system. In this study, we demonstrated that different spacer sequences vary in their ability to tolerate target mutations that allow phages and plasmids to escape from CRISPR-Cas immunity. These results uncover an unexpected complexity in the arms race between CRISPR-Cas systems and prokaryotic infectious genetic elements.
Using qualitative insights to change practice: exploring the culture of antibiotic prescribing and consumption for urinary tract infections
Authors: Duane Sinead , Domegan Christine , Callan Aoife , Galvin Sandra , Cormican Martin , Bennett Kathleen , Murphy Andrew W , Vellinga Akke 
Published: January 2016

ObjectivesThe aim of this paper is to explore the culture of antibiotic prescribing and consumption in the community for urinary tract infections (UTI) from the perspective of the general practitioners (GPs) and community member.DesignIndepth interviews were conducted with GPs, and focus groups were held with community members.SettingGeneral practice and community setting.Participants15 GPs practising in rural and urban locations in Ireland participated in the indepth interviews. 6 focus groups (n=42) with participants who had direct or indirect experiences with UTI were also undertaken.ResultsThe decision to prescribe or consume an antibiotic for a UTI is a set of complex processes including need recognition, information search and evaluation processes governed by the relationship and interactions between the GP and the patient. Different GP and patient decision-making profiles emerged emphasising the diversity and variety of general practice in real-life settings. The GP findings showed a requirement for more microbiological information on antibiotic resistance patterns to inform prescribing decisions. Focus group participants wanted a conversation with the GP about their illness and the treatment options available.ConclusionsCollectively, this research identified the consultation as a priority intervention environment for stimulating change in relation to antibiotics. This paper demonstrates how qualitative research can identify the interacting processes which are instrumental to the decision to prescribe or consume an antibiotic for a suspected UTI. Qualitative research empowers researchers to investigate the what, how and why of interventions in real-life setting. Qualitative research can play a critical and instrumental role in designing behavioural change strategies with high impact on practice. The results of this research were used to design a complex intervention informed by social marketing.Trial registration numberNCT01913860; Pre-results.
Cellulitis: Home Or Inpatient in Children from the Emergency Department (CHOICE): protocol for a randomised controlled trial
Authors: Ibrahim Laila F , Babl Franz E , Orsini Francesca , Hopper Sandy M , Bryant Penelope A 
Published: January 2016

IntroductionChildren needing intravenous antibiotics for cellulitis are usually admitted to hospital, whereas adults commonly receive intravenous treatment at home. This is a randomised controlled trial (RCT) of intravenous antibiotic treatment of cellulitis in children comparing administration of ceftriaxone at home with standard care of flucloxacillin in hospital. The study aims to compare (1) the rate of treatment failure at home versus hospital (2) the safety of treatment at home versus hospital; and (3) the effect of exposure to short course ceftriaxone versus flucloxacillin on nasal and gut micro-organism resistance patterns and the clinical implications.Methods and analysisInclusion criteria: children aged 6 months to <18 years with uncomplicated moderate/severe cellulitis, requiring intravenous antibiotics. Exclusions: complicated cellulitis (eg, orbital, foreign body) and immunosuppressed or toxic patients. The study is a single-centre, open-label, non-inferiority RCT. It is set in the emergency department (ED) at the Royal Children's Hospital (RCH) in Melbourne, Australia and the Hospital-in-the-Home (HITH) programme; a home-care programme, which provides outreach from RCH. Recruitment will occur in ED from January 2015 to December 2016. Participants will be randomised to either treatment in hospital, or transfer home under the HITH programme. The calculated sample size is 188 patients (94 per group) and data will be analysed by intention-to-treat.Primary outcome: treatment failure defined as a change in treatment due to lack of clinical improvement according to the treating physician or adverse events, within 48 hSecondary outcomes: readmission to hospital, representation, adverse events, length of stay, microbiological results, development of resistance, cost-effectiveness, patient/parent satisfaction. This study has started recruitment.Ethics and disseminationThis study has been approved by the Human Research Ethics Committee of the RCH Melbourne (34254C) and registered with the ClinicalTrials.gov registry (NCT02334124). We aim to disseminate the findings through international peer-reviewed journals and conferences.Clinical trialPre-results.
Comparing NICU teamwork and safety climate across two commonly used survey instruments
Authors: Profit Jochen , Lee Henry C , Sharek Paul J , Kan Peggy , Nisbet Courtney C , Thomas Eric J , Etchegaray Jason M , Sexton Bryan 
Published: January 2016

Background and objectivesMeasurement and our understanding of safety culture are still evolving. The objectives of this study were to assess variation in safety and teamwork climate and in the neonatal intensive care unit (NICU) setting, and compare measurement of safety culture scales using two different instruments (Safety Attitudes Questionnaire (SAQ) and Hospital Survey on Patient Safety Culture (HSOPSC)).MethodsCross-sectional survey study of a voluntary sample of 2073 (response rate 62.9%) health professionals in 44 NICUs. To compare survey instruments, we used Spearman's rank correlation coefficients. We also compared similar scales and items across the instruments using t tests and changes in quartile-level performance.ResultsWe found significant variation across NICUs in safety and teamwork climate scales of SAQ and HSOPSC (p<0.001). Safety scales (safety climate and overall perception of safety) and teamwork scales (teamwork climate and teamwork within units) of the two instruments correlated strongly (safety r=0.72, p<0.001; teamwork r=0.67, p<0.001). However, the means and per cent agreements for all scale scores and even seemingly similar item scores were significantly different. In addition, comparisons of scale score quartiles between the two instruments revealed that half of the NICUs fell into different quartiles when translating between the instruments.ConclusionsLarge variation and opportunities for improvement in patient safety culture exist across NICUs. Important systematic differences exist between SAQ and HSOPSC such that these instruments should not be used interchangeably.
Why do we still page each other? Examining the frequency, types and senders of pages in academic medical services
Authors: Carlile Narath , Rhatigan Joseph J , Bates David W 
Published: January 2016

BackgroundPaging still represents an important form of communication within hospitals, but it results in interruptions, and other more modern approaches could be superior. This study aims to describe how paging is currently used in an academic medical centre, including the frequency, type, urgency and sender of pages, so that improvements in communication can be better informed.Study sampleIn order to understand what communication needs paging fulfils in a modern academic medical centre, we analysed a database of 1252 pages sent to internal medicine residents within an academic medical centre. We assessed all pages from 3 separate general medicine rotations over a total of 56 days encompassing 602 h.ResultsResidents were paged an average of 22.4 times per day, with a maximum of 50 pages per day. Most pages were deemed clinically relevant (76%) and important (76%) to patient care. Overall, 59% of pages required a response. A mean of 7.7 pages were sent per patient, up to a maximum of 70 pages for one patient. Nurses (28%), consultants (16%) and the clinical laboratory (15%) were responsible for the majority of pages. Almost all pages from nurses (82%) and consultants (82%) required a response. Regionalised services had significantly fewer pages per day than non-regionalised services (19 vs 37, p≤0.00001).ConclusionsPaging remains widely used for communications within hospitals about patient care. Although the majority of pages were judged to be clinically relevant and important, they frequently required a response potentially leading to interruptions in workflow, and communication waste. Paging rate and volume has not decreased in 25 years despite significant penetration of newer technologies. For the majority of current uses of pages, we believe other approaches may now be more appropriate. Regionalisation significantly reduces the number and urgency of the pages.
Impact of the 2011 ACGME resident duty hour reform on hospital patient experience and processes-of-care
Authors: Rajaram Ravi , Saadat Lily , Chung Jeanette , Dahlke Allison , Yang Anthony D , Odell David D , Bilimoria Karl Y 
Published: January 2016

IntroductionIn 2011, the Accreditation Council for Graduate Medical Education (ACGME) expanded restrictions on resident duty hours. While studies have shown no association between these restrictions and improved outcomes, process-of-care and patient experience measures may be more sensitive to resident performance, and thus may be impacted by duty hour policies. The objective of this study was to evaluate the association between the 2011 resident duty hour reform and measures of processes-of-care and patient experience.MethodsHospital Consumer Assessment of Healthcare Providers and Systems survey data and process-of-care scores were obtained from the Centers for Medicare and Medicaid Services Hospital Compare website for 1 year prior to (1 July 2010 to 30 June 2011) and 1 year after (1 July 2011 to 30 June 2012) duty hour reform implementation. Using a difference-in-differences model, non-teaching and teaching hospitals were compared before and after the 2011 reform to test the association of this policy with changes in process-of-care and patient experience measure scores.ResultsDuty hour reform was not associated with a change in the five patient experience measures evaluated, including patients rating a hospital 9 or 10 (coefficient −0.003, 95% CI −0.79 to 0.79) or stating they would ‘definitely recommend’ a hospital (coefficient −0.28, 95% CI −1.01 to 0.44). For all 10 process-of-care measures examined, such as antibiotic timing (coefficient −0.462, 95% CI −1.502 to 0.579) and discontinuation (0.188, 95% CI −0.529 to 0.904), duty hour reform was not associated with a change in scores.ConclusionsThe 2011 ACGME duty hour reform was not associated with improvements in process-of-care and patient experience measures. These data should be considered when considering reform of resident duty hour policies.
Continuity of care and 30-day readmission for patients evaluated in the emergency room after cerebral aneurysm treatment
Authors: Bekelis Kimon , Missios Symeon , MacKenzie Todd A 
Published: January 2016

BackgroundThe association between continuity of care and the rate of 30-day readmissions after surgical procedures continues to be debated.ObjectiveTo investigate the association of 30-day readmissions with evaluation in the hospital where the original procedure was performed for patients presenting to the emergency department (ED) after cerebral aneurysm treatment.MethodsWe performed a cohort study of patients with cerebral aneurysms, who were evaluated in the ED within 30 days after discharge following surgical clipping or endovascular coiling between 2009 and 2013, and were registered in the Statewide Planning and Research Cooperative System database. A propensity score adjusted model was used to control for confounding, whereas mixed effects accounted for clustering at the hospital level.ResultsOf the 452 patients presenting to the ED, 218 (48.2%) were evaluated in a different hospital from that in which the original procedure was performed (7.7% readmitted), and 234 (51.8%) were evaluated at the original hospital (18.4% readmitted). In a multivariable analysis, we showed that evaluation in the ED of the original hospital was associated with decreased rate of 30-day readmission (OR=0.41; 95% CI 0.22 to 0.78). We found similar associations in a mixed-effects logistic regression model (OR=0.46; 95% CI 0.35 to 0.84) and a propensity score adjusted model (OR=0.41; 95% CI 0.22 to 0.77). This corresponds to10 patients needing to be evaluated in the hospital at which the original procedure was performed to prevent one readmission.ConclusionsUsing a comprehensive all-payer cohort of patients in New York State, who were evaluated in the ED after cerebral aneurysm treatment, we identified an association between assessment in the hospital at which the original procedure was performed and a lower rate of 30-day readmissions. This underlines the potential importance of continuity of care for surgical patients to prevent readmission.