bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistent Staphylococcus aureus Isolates from Two Independent Cases of Bacteremia Display Increased Bacterial Fitness and Novel Immune Evasion Phenotypes
Authors: Richards R. L. , Haigh R. D. , Pascoe B. , Sheppard S. K. , Price F. , Jenkins D. , Rajakumar K. , Morrissey J. A. 
Published: June 2015

ABSTRACT

Staphylococcus aureus
bacteremia cases are complicated by bacterial persistence and treatment failure despite the confirmed
in vitro
susceptibility of the infecting strain to administered antibiotics. A high incidence of methicillin-resistant
S. aureus
(MRSA) bacteremia cases are classified as persistent and are associated with poorer patient outcomes. It is still unclear how
S. aureus
evades the host immune system and resists antibiotic treatment for the prolonged duration of a persistent infection. In this study, the genetic changes and associated phenotypic traits specific to
S. aureus
persistent bacteremia were identified by comparing temporally dispersed isolates from persistent infections (persistent isolates) originating from two independent persistent
S. aureus
bacteremia cases with the initial infection isolates and with three resolved
S. aureus
bacteremia isolates from the same genetic background. Several novel traits were associated specifically with both independent sets of persistent
S. aureus
isolates compared to both the initial isolates and the isolates from resolved infections (resolved isolates). These traits included (i) increased growth under nutrient-poor conditions; (ii) increased tolerance of iron toxicity; (iii) higher expression of cell surface proteins involved in immune evasion and stress responses; and (iv) attenuated virulence in a
Galleria mellonella
larva infection model that was not associated with small-colony variation or metabolic dormancy such as had been seen previously. Whole-genome sequence analysis identified different single nucleotide mutations within the
mprF
genes of all the isolates with the adaptive persistence traits from both independent cases. Overall, our data indicate a novel role for MprF function during development of
S. aureus
persistence by increasing bacterial fitness and immune evasion.
A Plasmid-Borne System To Assess the Excision and Integration of Staphylococcal Cassette Chromosome
mec
Mediated by CcrA and CcrB
Authors: Wang Lei , Ahmed Mostafa H. , Safo Martin K. , Archer Gordon L. 
Published: June 2015

ABSTRACT

Resistance to methicillin and other β-lactam antibiotics in staphylococci is due to
mecA
, which is carried on a genomic island, staphylococcal cassette chromosome
mec
(SCC
mec
). The chromosomal excision and integration of SCC
mec
are mediated by the site-specific recombinase CcrAB or CcrC, encoded within this element. A plasmid-borne system was constructed to assess the activities of CcrA and CcrB in the excision and integration of SCC
mec
in
Escherichia coli
and
Staphylococcus aureus
. The excision frequency in
E. coli
mediated by CcrAB from methicillin-resistant
S. aureus
(MRSA) strain N315 was only 9.2%, while the integration frequency was 31.4%. In
S. aureus
the excision and integration frequencies were 11.0% and 18.7%, respectively. Truncated mutants identified the N-terminal domain of either CcrB or CcrA to be necessary for both integration and excision, while the C-terminal domain was important for recombination efficiency. Site-directed mutagenesis of the N-terminal domain identified S11 and R79 of CcrA and S16, R89, T149, and R151 of CcrB to be residues essential for catalytic activities, and the critical location of these residues was consistent with a model of the tertiary structure of the N terminus of CcrA and CcrB. Furthermore, CcrAB and CcrC, cloned from a panel of 6 methicillin-resistant
S. aureus
strains and 2 methicillin-resistant
Staphylococcus epidermidis
strains carrying SCC
mec
types II, IV, and V, also catalyzed integration at rates 1.3 to 10 times higher than the rates at which they catalyzed excision, similar to the results from N315. The tendency of SCC
mec
integration to be favored over excision may explain the low spontaneous excision frequency seen among MRSA strains.

IMPORTANCE
Spontaneous excision of the genomic island (SCCmec) that encodes resistance to beta-lactam antibiotics (methicillin resistance) in staphylococci would convert a methicillin-resistant strain to a methicillin-susceptible strain, improving therapy of difficult-to-treat infections. This study characterizes a model system by which the relative frequencies of excision and integration can be compared. Using a plasmid-based model for excision and integration mediated by the recombinases CcrA and CcrB, integration occurred at a higher frequency than excision, consistent with the low baseline excision frequency seen in most strains. This model system can now be used to study conditions and drugs that may raise the SCC
mec
excision frequency and generate strains that are beta-lactam susceptible.
Structures of Capsular Polysaccharide Serotypes 35F and 35C of Streptococcus pneumoniae Determined by Nuclear Magnetic Resonance and Their Relation to Other Cross-Reactive Serotypes
Authors: Bush C. Allen , Cisar John O. , Yang Jinghua 
Published: June 2015

ABSTRACTThe structures ofStreptococcus pneumoniaecapsular polysaccharides (CPSs) are essential for defining the antigenic as well as genetic relationships between CPS serotypes. The four serotypes that comprise CPS serogroup 35 (i.e., types 35F, 35A, 35B, and 35C) are known to cross-react with genetically related type 20, 29, 34, 42, or 47F. While the structures of CPS serotype 35A (CPS35A) and CPS35B are known, those of CPS35F and CPS35C are not. In the present study, the serotypes of CPS35F and CPS35C were characterized by high-resolution heteronuclear magnetic resonance (NMR) spectroscopy and glycosyl composition analyses to reveal the following repeat unit structures:where OAc indicates O-acetylated. Importantly, CPS35F, the immunizing serotype for the production of group 35 serum, more closely resembles CPS34 and CPS47F than other members of serogroup 35. Moreover, CPS35C is distinct from either CPS35F or CPS35B but closely related to CPS35A and identical to de-O-acetylated CPS42. The findings provide a comprehensive view of the structural and genetic relations that exist between the members of CPS serogroup 35 and other cross-reactive serotypes.IMPORTANCECross-reactions of diagnostic rabbit antisera withStreptococcus pneumoniaecapsular polysaccharide serotypes are generally limited to members of the same serogroup. Exceptions do, however, occur, most notably among a group of nonvaccine serotypes that includes the members of serogroup 35 (i.e., types 35F, 35A, 35B, and 35C) and other genetically related types. The presently determined structures ofS. pneumoniaeserotypes 35F and 35C complete the structural characterization of serogroup 35 and thereby provide the first comprehensive description of how different members of this serogroup are related to each other and to types 29, 34, 42, and 47F. The structural and genetic features of these serotypes suggest the existence of three distinct capsular polysaccharide subgroups that presumably emerged by immune selection in the human host.
Characterization of an Unconventional Rhodopsin from the Freshwater Actinobacterium Rhodoluna lacicola
Authors: Keffer J. L. , Hahn M. W. , Maresca J. A. 
Published: June 2015

ABSTRACT

Rhodopsin-encoding microorganisms are common in many environments. However, knowing that rhodopsin genes are present provides little insight into how the host cells utilize light. The genome of the freshwater actinobacterium
Rhodoluna lacicola
encodes a rhodopsin of the uncharacterized actinorhodopsin family. We hypothesized that actinorhodopsin was a light-activated proton pump and confirmed this by heterologously expressing
R. lacicola
actinorhodopsin in retinal-producing
Escherichia coli
. However, cultures of
R. lacicola
did not pump protons, even though actinorhodopsin mRNA and protein were both detected. Proton pumping in
R. lacicola
was induced by providing exogenous retinal, suggesting that the cells lacked the retinal cofactor. We used high-performance liquid chromatography (HPLC) and oxidation of accessory pigments to confirm that
R. lacicola
does not synthesize retinal. These results suggest that in some organisms, the actinorhodopsin gene is constitutively expressed, but rhodopsin-based light capture may require cofactors obtained from the environment.

IMPORTANCE
Up to 70% of microbial genomes in some environments are predicted to encode rhodopsins. Because most microbial rhodopsins are light-activated proton pumps, the prevalence of this gene suggests that in some environments, most microorganisms respond to or utilize light energy. Actinorhodopsins were discovered in an analysis of freshwater metagenomic data and subsequently identified in freshwater actinobacterial cultures. We hypothesized that actinorhodopsin from the freshwater actinobacterium
Rhodoluna lacicola
was a light-activated proton pump and confirmed this by expressing actinorhodopsin in retinal-producing
Escherichia coli
. Proton pumping in
R. lacicola
was induced only after both light and retinal were provided, suggesting that the cells lacked the retinal cofactor. These results indicate that photoheterotrophy in this organism and others may require cofactors obtained from the environment.
Clostridium difficile PCR Ribotype 018, a Successful Epidemic Genotype
Authors: Baldan Rossella , Trovato Alberto , Bianchini Valentina , Biancardi Anna , Cichero Paola , Mazzotti Maria , Nizzero Paola , Moro Matteo , Ossi Cristina , Scarpellini Paolo , Cirillo Daniela Maria 
Published: June 2015

ABSTRACT

Clostridium difficile
infection (CDI) became a public health problem for the global spreading of the so-called hypervirulent PCR ribotypes (RTs) 027 and 078, associated with increases in the transmission and severity of the disease. However, especially in Europe, several RTs are prevalent, and the concept of hypervirulence is currently debated. We investigated the toxin and resistance profiles and the genetic relatedness of 312
C. difficile
strains isolated in a large Italian teaching hospital during a 5-year period. We evaluated the role of CDI-related antibiotic consumption and infection control practices on the RT predominance in association with their molecular features and transmission capacity. Excluding secondary cases due to nosocomial transmission, RT018 was the predominant genotype (42.4%) followed by RT078 (13.6%), while RT027 accounted for 0.8% of the strains. RT078 was most frequently isolated from patients in intensive care units. Its prevalence significantly increased over time, but its transmission capacity was very low. In contrast, RT018 was highly transmissible and accounted for 95.7% of the secondary cases. Patients with the RT018 genotype were significantly older than those with RT078 and other RTs, indicating an association between epidemic RT and age. We provide here the first epidemiological evidence to consider RT018 as a successful epidemic genotype that deserves more attention in clinical practice.
Examination of the Enterotoxigenic Escherichia coli Population Structure during Human Infection
Authors: Sahl Jason W. , Sistrunk Jeticia R. , Fraser Claire M. , Hine Erin , Baby Nabilah , Begum Yasmin , Luo Qingwei , Sheikh Alaullah , Qadri Firdausi , Fleckenstein James M. , Rasko David A. 
Published: June 2015

ABSTRACT

Enterotoxigenic
E. coli
(ETEC) can cause severe diarrhea and death in children in developing countries; however, bacterial diversity in natural infection is uncharacterized. In this study, we explored the natural population variation of ETEC from individuals with cholera-like diarrhea. Genomic sequencing and comparative analysis of multiple ETEC isolates from twelve cases of severe diarrhea demonstrated clonal populations in the majority of subjects (10/12). In contrast, a minority of individuals (2/12) yielded phylogenomically divergent ETEC isolates. Detailed examination revealed that isolates also differed in virulence factor content. These genomic data suggest that severe, cholera-like ETEC infections are largely caused by a clonal population of organisms within individual patients. Additionally, the isolation of similar clones from geographically and temporally dispersed cases with similar clinical presentations suggests that some isolates are particularly suited for virulence. The identification of multiple genomically diverse isolates with variable virulence factor profiles from a single subject highlights the dynamic nature of ETEC, as well as a potential weakness in the examination of cultures obtained from a single colony in clinical settings. These findings have implications for vaccine design and provide a framework for the study of population variation in other human pathogens.

IMPORTANCE
Enterotoxigenic
Escherichia coli
(ETEC) has been identified as one of the major causes of diarrheal diseases in children as well as travelers. It has been previously appreciated that this pathogenic variant of
E. coli
is diverse, both at the genomic level, as defined with multilocus sequence typing, and with regard to the presence or absence of virulence factors within clonal groups. Using whole-genome sequencing and comparative analysis, we identified and characterized diverse enterotoxigenic
E. coli
isolates from individual patients. In 17% of patients, we identified multiple distinct ETEC isolates, each with unique genomic features and in some cases diverse virulence factor profiles. These studies ascertained that any one person may be colonized by multiple pathogenic ETEC isolates, which may impact how we think about the development of vaccines and therapeutics against these organisms.
The Atypical Occurrence of Two Biotin Protein Ligases in Francisella novicida Is Due to Distinct Roles in Virulence and Biotin Metabolism
Authors: Feng Youjun , Chin Chui-Yoke , Chakravartty Vandana , Gao Rongsui , Crispell Emily K. , Weiss David S. , Cronan John E. 
Published: June 2015

ABSTRACT

The physiological function of biotin requires biotin protein ligase activity in order to attach the coenzyme to its cognate proteins, which are enzymes involved in central metabolism. The model intracellular pathogen
Francisella novicida
is unusual in that it encodes two putative biotin protein ligases rather than the usual single enzyme.
F. novicida
BirA has a ligase domain as well as an N-terminal DNA-binding regulatory domain, similar to the prototypical BirA protein in
E. coli
. However, the second ligase, which we name BplA, lacks the N-terminal DNA binding motif. It has been unclear why a bacterium would encode these two disparate biotin protein ligases, since
F. novicida
contains only a single biotinylated protein.
In vivo
complementation and enzyme assays demonstrated that BirA and BplA are both functional biotin protein ligases, but BplA is a much more efficient enzyme. BirA, but not BplA, regulated transcription of the biotin synthetic operon. Expression of
bplA
(but not
birA
) increased significantly during
F. novicida
infection of macrophages. BplA (but not BirA) was required for bacterial replication within macrophages as well as in mice. These data demonstrate that
F. novicida
has evolved two distinct enzymes with specific roles; BplA possesses the major ligase activity, whereas BirA acts to regulate and thereby likely prevent wasteful synthesis of biotin. During infection BplA seems primarily employed to maximize the efficiency of biotin utilization without limiting the expression of biotin biosynthetic genes, representing a novel adaptation strategy that may also be used by other intracellular pathogens.

IMPORTANCE
Our findings show that
Francisella novicida
has evolved two functional biotin protein ligases, BplA and BirA. BplA is a much more efficient enzyme than BirA, and its expression is significantly induced upon infection of macrophages. Only BplA is required for
F. novicida
pathogenicity, whereas BirA prevents wasteful biotin synthesis. These data demonstrate that the atypical occurrence of two biotin protein ligases in
F. novicida
is linked to distinct roles in virulence and biotin metabolism.
Scoping review of physical rehabilitation interventions in long-term care: protocol for tools, models of delivery, outcomes and quality indicators
Authors: McArthur Caitlin , Gibbs Jenna , Papaioannou Alexandra , Hirdes John , Milligan James , Berg Katherine , Giangregorio Lora 
Published: June 2015

IntroductionA growing number of medically complex older adults reside in long-term care (LTC) and often require physical rehabilitation (PR). While PR is effective at maintaining or improving a patient's physical function, the breadth of PR interventions evaluated in LTC, which outcomes or quality indicators (QI) can be used to evaluate PR, and what tools or models can be used to determine eligibility for PR services remain unknown.Methods and analysisA scoping review will be conducted to address the following research questions: (1) What types of PR have been evaluated for efficacy or effectiveness in LTC? (2) Which outcomes or QIs have been used when evaluating PR interventions in LTC, and how can this inform evaluation of PR using existing QIs in the Canadian context? (3) What tools or models exist or have been validated for decision-making in the allocation of PR resources in LTC? We will conduct a comprehensive literature search in MEDLINE, EMBASE, CINAHL, Cochrane Database of Systematic Reviews, Physiotherapy Evidence Database (PEDro) and Occupational Therapy Systematic Evaluation of Evidence database (OTseeker) and a structured grey literature search. Two team members will screen articles and abstract the data. The results will be displayed according to the research question they address. Data abstracted regarding outcomes and QIs will be mapped onto existing, publicly reported QIs used in Ontario, Canada.Ethics and disseminationThe scoping review will synthesise the characteristics of PR interventions described in the literature, the outcomes used to evaluate them and tools to determine eligibility for services. The review will be the first step in formally identifying what outcomes and QIs have been used to evaluate PR in LTC, and will be used to inform a stakeholder consensus process exploring the same question. The scoping review may also identify knowledge gaps. The results will be disseminated via publication and presentation at conferences, in addition to a 1-day stakeholder meeting.
Safer Wards: reducing violence on older people's mental health wards
Authors: Brown Juliette , Fawzi Waleed , McCarthy Cathy , Stevenson Carmel , Kwesi Solomon , Joyce Maggie , Dusoye Jenny , Mohamudbucus Yasin , Shah Amar 
Published: June 2015

AbstractThrough the Safer Wards project we aimed to reduce the number of incidents of physical violence on older people’s mental health wards. This was done using quality improvement methods and supported by the Trust’s extensive programme of quality improvement, including training provided by the Institute for Healthcare Improvement. Violence can be an indicator of unmet needs in this patient population, with a negative effect on patient care and staff morale. Reducing harm to patients and staff is a strategic aim of our Trust.We established a multi-disciplinary group who led on the project on each ward and used a Pareto diagram to establish the focus of our work. We established a dashboard of measures based on our incident reporting system Datix, including number of incidents of violence, days between incidents, days of staff sickness, days between staff injury, use of restraint, and use of rapid tranquilisation (the last two being balancing measures in the reduction of violence). Each team identified factors driving physical violence on the wards, under headings of unmet patient needs, staff needs and staff awareness, which included lack of activity and a safe and therapeutic environment.Using driver diagrams, we identified change ideas that included hourly rounding (proactive checks on patient well-being), the addition of sensory rooms, flexible leave for patients, and a structured activity programme. We also introduced exercise to music, therapeutic groups led by patients, and focused on discharge planning and pet therapy, each of which starting sequentially over the course of a one year period from late 2013 and subject to a cycle of iterative learning using PDSA methods.The specific aim was a 20% decrease in violent incidents on three wards in City and Hackney, and Newham. Following our interventions, days between violent incidents increased from an average of three to an average of six. Days between staff injury due to physical violence rose from an average of eight (one violent incident resulting in staff injury every eight days) to 22 (one incident every 22 days). Incidents of physical violence reduced from 63 in 2013 to 39 in 2014. We were also able to quantify reduced costs associated with reduction in violence.The success of this project in our view lay in the involvement of ward staff in understanding the problems and generating local solutions which were also broadly evidenced based. Patients were also closely involved in generating ideas. We are currently incorporating much of this work into routine practice in order to sustain improvement, as well as continuing to generate new ideas for further improvement while using the skills learnt in this process to address other problems.
Factors associated with RTCs among for-hire three-wheeler drivers in Sri Lanka: a case–control study
Authors: Jayatilleke Achala Upendra , Poudel Krishna C , Dharmaratne Samath D , Jayatilleke Achini C , Jimba Masamine 
Published: June 2015

ObjectiveFor-hire three-wheeler crashes are a growing burden in Sri Lanka. We conducted this study to examine the factors associated with road traffic crashes (RTCs) among for-hire three-wheeler drivers in Sri Lanka.MethodsWe conducted a case–control study in Kandy, Sri Lanka between August 2008 and March 2009. Cases were all the for-hire three-wheeler drivers involved in crashes in Kandy between 1 January and 31 December 2007 (n=88). Controls were non-crash-involved for-hire three-wheeler drivers in Kandy, matched to the ages of the cases (n=88). We examined participants’ sociodemographic characteristics, job characteristics, driving behaviours and the characteristics of their three wheelers. We used conditional logistic regression analysis to examine the factors associated with for-hire three-wheeler crashes.ResultsThree factors were positively associated with for-hire three-wheeler crashes. They were as follows: taking more than three passengers in the passenger seat (adjusted OR (AOR)=8.03, 95% CI 1.16 to 55.71), higher age of the three wheelers (AOR=1.38, 95% CI 1.04 to 1.84), and being convicted by police for traffic law violations during the past 12 months (AOR=1.74, 95% CI 1.16 to 2.58).ConclusionsWe identified three factors that might lead to for-hire three-wheeler crashes in Sri Lanka. They were as follows: carrying excessive passengers, higher three-wheeler age and drivers’ traffic law violations. To prevent three-wheeler crashes, laws should prevent three wheelers carrying more than three passengers. Yearly examinations should be mandated to ensure proper driving conditions of for-hire three wheelers. Police should enforce traffic laws to prevent traffic law violations by three-wheeler drivers.