bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changing Epidemiology ofClostridium difficile-Associated Disease in Children
Authors: Benson Lacey , Song Xiaoyan , Campos Joseph , Singh Nalini 
Published: October 2007

Objective.To determine temporal trends in the incidence rate forClostridium difficile-associated disease (CDAD) in a pediatric patient population.Methods.We performed an observational, retrospective cohort study that included children who visited or were admitted to Children's National Medical Center during the period from July 2001 through June 2006. The CDAD incidence rates were determined and examined for changes over time using the Poisson regression method.Results.A total of 513 patients whose stool specimens tested positive forC. difficiletoxin were identified. Of these patients, 61% were children aged 2 years or older. The proportion of patients with CDAD in this age group has steadily increased from 46% in 2001 to 64% in 2006. Largely as a result of an increasing number of cases of community-associated CDAD, the incidence of CDAD increased significantly in the outpatient setting, particularly in the emergency department (1.18 cases per 1,000 visits in 2001 vs 2.47 cases per 1,000 visits in 2006;P= .02). The incidence among inpatients decreased during the study period (1.024 cases per 1,000 patient-days in 2001 vs 0.680 cases per 1,000 patient-days in 2006;P= .004). In the neonatal intensive care unit,C. difficile toxinwas detected in stool specimens collected from 22 patients aged from 15 days to 6 months.Conclusion.This study revealed a steady increase in the number of patients seen in the emergency department with community-acquired CDAD. Findings from this study suggest that the characteristics of CDAD in children—a population that has not been considered to be at high risk for this disease in the past—are changing. Further investigations are warranted to explore deviations from the established burdens of the disease and patient risk factors.
Skin, Soft Tissue, Bone, and Joint Infections in Hospitalized Patients: Epidemiology and Microbiological, Clinical, and Economic Outcomes
Authors: Lipsky Benjamin A. , Weigelt John A. , Gupta Vikas , Killian Aaron , Peng Michael M. 
Published: October 2007

Background.Infections involving skin, soft tissue, bone, or joint (SSTBJ) are common and often require hospitalization. There are currently few published studies on the epidemiology and clinical and economic outcomes of these infections, whether acquired in the community or healthcare setting, in a large population.Objective.To characterize outcomes of culture-proven SSTBJ infection in hospitalized patients, using information from a large database.Design.We identified patients hospitalized in 134 institutions during 2002-2003 for whom specific International Classification of Diseases, Ninth Revision, Clinical Modification diagnosis codes and a culture-positive SSTBJ specimen were recorded. Patients were classified into 4 clinical groups based on the type and clinical severity of infection. Patients in each group were further classified on the basis of whether their infection was community acquired or healthcare associated and whether it was complicated or uncomplicated.Results.We identified 12,506 patients with culture-positive infections and categorized them as having cellulitis (37.3%), osteomyelitis or septic arthritis (22.4%), surgical wound infection (26.1%), device-associated or prosthesis infection (7.2%), or other SSTBJ infection (6.9%). Monomicrobial infection was reported for 59% of patients, 54.6% of whom had Staphylococcus aureus as the etiologic agent. Of all S. aureus isolates recovered, 1,121 (28.0%) of 4,007 were resistant to methicillin. Healthcare-associated infections accounted for 27.2% of cases and were associated with a significantly greater mortality rate, a longer length of stay, and greater hospital charges, compared with community-acquired infections. Patients with a complicated infection (78.4%) had a significantly greater mortality rate, a longer length of stay, and greater hospital charges, compared with patients with an uncomplicated infection.Conclusions.SSTBJ infections are frequent among hospitalized patients. S. aureus caused infection in more than 50% of the patients studied, and 28.0% of the S. aureus isolates recovered were resistant to methicillin. Healthcare-associated and complicated infections are associated with a significantly higher mortality rate and more prolonged and expensive hospitalizations. These findings could assist in projects to revise current management strategies in order to optimize outcomes while restraining costs.
Case-Control Study of Surgical Site Infections Associated With Pacemakers and Implantable Cardioverter-Defibrillators
Authors: Marschall Jonas , Hopkins-Broyles Diane , Jones Marilyn , Fraser Victoria J. , Warren David K. 
Published: October 2007

Objective.In 2000, the rate of surgical site infections (SSIs) associated with pacemaker and implantable cardioverter-defibrillator (ICD) procedures performed in the cardiothoracic operating rooms of hospital A was 16% (19 of 116 procedures resulted in infections). This study investigates risks for SSI associated with these procedures in the cardiothoracic operating room.Design.Unmatched 1: 3 case-control study performed over a 12-month period among patients who had undergone implantation of a pacemaker and/or ICD. A standardized observation scrutinized infection control practices in the area where the procedures were performed.Setting.The cardiothoracic operating rooms of hospital A, which belongs to a hospital consortium in the midwestern United States.Patients.Patients with SSI were identified as case patients. Control patients were chosen from the group of uninfected patients who had procedures performed during the same period as case patients.Results.A total of 19 SSIs associated with pacemaker and ICD procedures were retrospectively identified among the patients who underwent procedures in these cardiothoracic operating rooms. Culture samples were obtained from 7 patients; 2 yielded coagulase-negativeStaphylococcuson culture, 2 yieldedStaphylococcus aureus, 1 yieldedSerratia marcescens, and 2 showed no growth. In the case-control study, age, race, sex, diabetes mellitus, smoking history, timing of antibiotic therapy, and hair removal did not differ significantly between case patients and control patients. Case patients were more likely to have an abdominal device in place (odds ratio [OR], 5.5 [95% confidence interval {CI}, 1.6-19.3];P= .006) and less likely to have received a new implant (OR 0.3 [95% CI, 0.1-0.8];P= .02) or to have had new leads placed (OR, 0.2 [95% CI, 0.1-0.6];P= .003).Conclusions.Abdominal placement of implanted devices was associated with occurrence of an SSI after pacemaker and/or ICD procedures.
Infection Control Policies and Practices for Iowa Long-Term Care Facility Residents With Clostridium difficile Infection
Authors: Quinn Laura K. , Chen Yiyi , Herwaldt Loreen A. 
Published: October 2007

Objective.To identify infection control policies and practices used by Iowa long-term care facilities (LTCFs) for residents with Clostridium difficile infection or C. difficile-associated diarrhea and to assess use of antimicrobial agents.Design.Survey.Setting.LTCFs in Iowa that responded between March 25, 2005 (ie, when surveys were mailed), and July 2005.Results.Of the 418 LTCFs in Iowa, 263 (62.9%) responded. Most facilities (94.3%) reported that they accept persons known to have C. difficile infection. Few LTCFs reported that clusters of C. difficile infection had been identified. However, only 111 facilities (42.2%) had a protocol to identify residents with C. difficile infection, and most (77.5%) did not test for C. difficile unless a resident had severe diarrhea. Only 58.5% of the facilities placed residents with C. difficile infection in private rooms, and 60.9% cohorted residents infected with C. difficile with other residents with C. difficile colonization or infection. Only 66 facilities (25.1%) have a program to control the use of antimicrobial agents. Staff could use alcohol-based hand gel products after contact with residents known to have C. difficile infection (in 188 facilities [71.5%]) or diarrhea (in 173 [65.8%]). However, the survey did not ask whether the staff used alcohol-based products instead of soap and water.Conclusions.C. difficile is present in Iowa LTCFs, but many C. difficile infections probably remain undiagnosed. Staff in LTCFs should be educated about this organism so that they can implement appropriate testing and preventive strategies.
Healthcare Workers' Knowledge and Attitudes About Pertussis and Pertussis Vaccination
Authors: Goins William P. , Schaffner William , Edwards Kathryn M. , Talbot Thomas R. 
Published: October 2007

Objective.To determine knowledge and attitudes about pertussis and pertussis vaccination among healthcare workers (HCWs).Design.Self-administered, Web-based survey.Setting.Tertiary-care academic medical center.Participants.Medical center employees who participated in direct patient care were recruited to complete the survey through institutional e-mail.Results.Of 14,893 potentially eligible employees, 1,819 (12%) completed the survey. Most respondents (87%) did not plan to receive the pertussis vaccine. Intent to receive vaccination (which included recent history of vaccination) was associated with the following 4 factors: receipt of a physician recommendation for vaccination (odds ratio [OR], 9.01), awareness of Centers for Disease Control and Prevention recommendations for pertussis vaccination for HCWs (OR, 6.89), receipt of encouragement to be vaccinated from a coworker (OR, 4.72), the belief that HCWs may spread pertussis to patients and family (OR, 1.80). Two factors were negatively associated with intent to receive vaccination: the presence of children in the HCW's home (OR, 0.69) and employment as a nurse (OR, 0.59). Reasons cited by those who did not intend to receive vaccination included lack of a personal recommendation for vaccination (78%), receipt of vaccination as a child (51%), and perception that there was no significant risk for contracting pertussis (38%).Conclusions.Of the HCWs surveyed, only 13% intended to receive the pertussis vaccine. A perceived lack of recommendation for vaccination and inaccurate conceptions about pertussis and pertussis vaccination were cited as reasons HCWs did not intend to be vaccinated. Institutional pertussis vaccination campaigns should focus on the risks of healthcare-associated pertussis and new recommendations for pertussis vaccination.
Impact of Contact and Droplet Precautions on the Incidence of Hospital-Acquired Methicillin-Resistant Staphylococcus aureus Infection
Authors: Mangini Ed , Segal-Maurer Sorana , Burns Janice , Avicolli Annette , Urban Carl , Mariano Noriel , Grenner Louise , Rosenberg Carl , Rahal James J. 
Published: October 2007

Objective.To evaluate the efficacy of contact and droplet precautions in reducing the incidence of hospital-acquired methicillin-resistant Staphylococcus aureus (MRSA) infections.Design.Before-after study.Setting.A 439-bed, university-affiliated community hospital.Methods.To identify inpatients infected or colonized with MRSA, we conducted surveillance of S. aureus isolates recovered from clinical culture and processed by the hospital's clinical microbiology laboratory. We then reviewed patient records for all individuals from whom MRSA was recovered. The rates of hospital-acquired MRSA infection were tabulated for each area where patients received nursing care. After a baseline period, contact and droplet precautions were implemented in all intensive care units (ICUs). Reductions in the incidence of hospital-acquired MRSA infection in ICUs led to the implementation of contact precautions in non-ICU patient care areas (hereafter, “non-ICU areas”), as well. Droplet precautions were discontinued. An analysis comparing the rates of hospital-acquired MRSA infection during different intervention periods was performed.Results.The combined baseline rate of hospital-acquired MRSA infection was 10.0 infections per 1,000 patient-days in the medical ICU (MICU) and surgical ICU (SICU) and 0.7 infections per 1,000 patient-days in other ICUs. Following the implementation of contact and droplet precautions, combined rates of hospital-acquired MRSA infection in the MICU and SICU decreased to 4.3 infections per 1,000 patient-days (95% confidence interval [CI], 0.17-0.97; P = .03). There was no significant change in hospital-acquired MRSA infection rates in other ICUs. After the discontinuation of droplet precautions, the combined rate in the MICU and SICU decreased further to 2.5 infections per 1,000 patient-days. This finding was not significant (P = .43). In the non-ICU areas that had a high incidence of hospital-acquired MRSA infection, the rate prior to implementation of contact precautions was 1.3 infections per 1,000 patient-days. After the implementation of contact precautions, the rate in these areas decreased to 0.9 infections per 1,000 patient-days (95% CI, 0.47-0.94; P = .02).Conclusion.The implementation of contact precautions significantly decreased the rate of hospital-acquired MRSA infection, and discontinuation of droplet precautions in the ICUs led to a further reduction. Additional studies evaluating specific infection control strategies are needed.
Epidemiologic, Clinical, and Economic Evaluation of an Outbreak of Clonal Multidrug-ResistantAcinetobacter baumanniiInfection in a Surgical Intensive Care Unit
Authors: Young Lisa S. , Sabel Allison L. , Price Connie S. 
Published: October 2007

Objectives.To determine risk factors for acquisition of multidrug-resistant (MDR)Acinetobacter baumanniiinfection during an outbreak, to describe the clinical manifestations of infection, and to ascertain the cost of infection.Design.Case-control study.Setting.Surgical intensive care unit in a 400-bed urban teaching hospital and level 1 trauma center.Patients.Case patients received a diagnosis of infection due toA. baumanniiisolates with a unique pattern of drug resistance (ie, susceptible to imipenem, variably susceptible to aminoglycosides, and resistant to all other antibiotics) between December 1, 2004, and August 31, 2005. Case patients were matched 1 : 1 with concurrently hospitalized control patients. Isolates' genetic relatedness was established by pulsed-field gel electrophoresis.Results.Sixty-seven patients met the inclusion criteria. Case and control patients were similar with respect to age, duration of hospitalization, and Charlson comorbidity score. MDRA. baumanniiinfections included ventilator-associated pneumonia (in 56.7% of patients), bacteremia (in 25.4%), postoperative wound infections (in 25.4%), central venous catheter-associated infections (in 20.9%), and urinary tract infections (in 10.4%). Conditional multiple logistic regression was used to determine statistically significant risk factors on the basis of results from the bivariate analyses. The duration of hospitalization and healthcare charges were modeled by multiple linear regression. Significant risk factors included higher Acute Physiology and Chronic Health Evaluation II score (odds ratio [OR], 1.1 per point increase;P= .06), duration of intubation (OR, 1.4 per day intubated;P<.01), exposure to bronchoscopy (OR, 22.7;P= .03), presence of chronic pulmonary disease (OR, 77.7;P= .02), receipt of fluconazole (OR, 73.3;P<.01), and receipt of levofloxacin (OR, 11.5;P= .02). Case patients had a mean of $60,913 in attributable excess patient charges and a mean of 13 excess hospital days.Interventions.Infection control measures included the following: limitations on the performance of pulsatile lavage wound debridement, the removal of items with upholstered surfaces, and the implementation of contact isolation for patients with suspected MDRA. baumanniiinfection.Conclusions.This large outbreak of infection due to clonal MDRA. baumanniicaused significant morbidity and expense. Aerosolization of MDRA. baumanniiduring pulsatile lavage debridement of infected wounds and during the management of respiratory secretions from colonized and infected patients may promote widespread environmental contamination. Multifaceted infection control interventions were associated with a decrease in the number of MDRA. baumanniiisolates recovered from patients.
Factors Associated With Critical-Care Healthcare Workers' Adherence to Recommended Barrier Precautions During the Toronto Severe Acute Respiratory Syndrome Outbreak
Authors: Shigayeva A. , Green K. , Raboud J. M. , Henry B. , Simor A. E. , Vearncombe M. , Zoutman D. , Loeb M. , McGeer A. ,   SARS Hospital Investigation Team
Published: October 2007

Objective.To assess factors associated with adherence to recommended barrier precautions among healthcare workers (HCWs) providing care to critically ill patients with severe acute respiratory syndrome (SARS).Setting.Fifteen acute care hospitals in Ontario, CanadaDesign.Retrospective cohort study.Patients.All patients with SARS who required intubation during the Toronto SARS outbreak in 2003.Participants.HCWS who provided care to or entered the room of a SARS patient during the period from 24 hours before intubation until 4 hours after intubation.Methods.Standardized interviews were conducted with eligible HCWs to assess their interactions with the SARS patient, their use of barrier precautions, their practices for removing personal protective equipment, and the infection control training they received.Results.Of 879 eligible HCWs, 795 (90%) participated. In multivariate analysis, the following predictors of consistent adherence to recommended barrier precautions were identified: recognition of the patient as a SARS case (odds ratio [OR], 2.5 [95% confidence interval {CI}, 1.5-4.5); recent infection control training (OR for interactive training, 2.7 [95% CI, 1.7-4.4]; OR for passive training, 1.7 [95% CI, 1.0-3.0]), and working in a SARS unit (OR, 4.0 [95% CI, 1.8-8.9]) or intensive care unit (OR, 4.3 [95% CI, 2.0-9.0]). Two factors were associated with significantly lower rates of consistent adherence: the provision of care for patients with higher Acute Physiology and Chronic Health Evaluation (APACHE) II scores (OR for score APACHE II of 20 or greater, 0.4 [95% CI, 0.28-0.68]) and work on shifts that required more frequent room entry (OR for 6 or more entries per shift, 0.5 [95% CI, 0.32-0.86]).Conclusions.There were significant deficits in knowledge about self-protection that were partially corrected by education programs during the SARS outbreak. HCWs' adherence to self-protection guidelines was most closely associated with whether they provided care to patients who had received a definite diagnosis of SARS.
Epidemiology of Multidrug-Resistant Bacteria in Patients With Long Hospital Stays
Authors: Buke Cagri , Armand-Lefevre Laurence , Lolom Isabelle , Guerinot Waafa , Deblangy Claude , Ruimy Raymond , Andremont Antoine , Lucet Jean-Christophe 
Published: October 2007

Objective.To determine rates of colonization with multidrug-resistant (MDR) bacteria (ie, methicillin-resistantStaphylococcus aureus[MRSA], vancomycin-resistantEnterococcus[VRE], extended-spectrum β-lactamase [ESBL]-producing Enterobacteriaceae, andAcinetobacter baumannii) after prolonged hospitalization and to assess the yield of surveillance cultures and variables associated with colonization with MDR bacteria.Design.Prospective observational cohort study conducted from February 6 to May 26, 2006.Methods.All patients who spent more than 30 days in our university hospital (Paris, France) were included. Rectal and nasal swab samples obtained during day 30 screening were examined for MRSA, VRE, ESBL-producing Enterobacteriaceae, andA. baumannii.Results.Of 470 eligible patients, 439 had surveillance culture samples available for analysis, including 51 patients (11.6%) with a history of colonization or infection due to 1 or more types of MDR bacteria (MRSA, recovered from 35 patients; ESBL-producing Enterobacteriaceae, from 16 patients;A. baumannii, from 6 patients; and VRE, from 0 patients) and 37 patients (9.5% of the 388 patients not known to have any of the 4 MDR bacteria before day 30 screening) newly identified as colonized by 1 or more MDR bacteria (MRSA, recovered from 20 patients; ESBL-producing Enterobacteriaceae, from 16 patients;A. baumannii, from 1 patient; and VRE, from 0 patients). A total of 87 (19.8%) of 439 patients were identified as colonized or infected with MDR bacteria at day 30. Factors that differed between patients with and without MRSA colonization included age, McCabe score, comorbidity score, receipt of surgery, and receipt of fluoroquinolone treatment. Patients with ESBL-producing Enterobacteriaceae colonization were younger than patients with MRSA colonization.Conclusions.Differences in the variables associated with MRSA colonization and ESBL-producing Enterobacteriaceae colonization suggest differences in the epidemiology of these 2 organisms. Day 30 screening resulted in a 72.5% increase in the number of patients identified as colonized with at least 1 type of MDR bacteria.
i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles
Authors: Simillion Cedric , Janssens Koen , Sterck Lieven , Van de Peer Yves 
Published: October 2007

Abstract
Summary: i-ADHoRe is a software tool that combines gene content and gene order information of homologous genomic segments into profiles to detect highly degenerated homology relations within and between genomes. The new version offers, besides a significant increase in performance, several optimizations to the algorithm, most importantly to the profile alignment routine. As a result, the annotations of multiple genomes, or parts thereof, can be fed simultaneously into the program, after which it will report all regions of homology, both within and between genomes.
Availability: The i-ADHoRe 2.0 package contains the C++ source code for the main program as well as various Perl scripts and a fully documented Perl API to facilitate post-processing. The software runs on any Linux- or -UNIX based platform. The package is freely available for academic users and can be downloaded from http://bioinformatics.psb.ugent.be/
Contact: yves.vandepeer@psb.ugent.be
Supplementary information: Supplementary data are available at Bioinformatics online.
OsMADS51 Is a Short-Day Flowering Promoter That Functions Upstream of Ehd1, OsMADS14, and Hd3a
Authors: Kim Song Lim , Lee Shinyoung , Kim Hyo Jung , Nam Hong Gil , An Gynheung 
Published: October 2007

Abstract
Although flowering regulatory mechanisms have been extensively studied in Arabidopsis (Arabidopsis thaliana), those in other species have not been well elucidated. Here, we investigated the role of OsMADS51, a type I MADS-box gene in the short-day (SD) promotion pathway in rice (Oryza sativa). In SDs OsMADS51 null mutants flowered 2 weeks later than normal, whereas in long days loss of OsMADS51 had little effect on flowering. Transcript levels of three flowering regulators—Ehd1, OsMADS14, and Hd3a—were decreased in these mutants, whereas those of OsGI and Hd1 were unchanged. Ectopic expression of OsMADS51 caused flowering to occur about 7 d earlier only in SDs. In ectopic expression lines, transcript levels of Ehd1, OsMADS14, and Hd3a were increased, but those of OsGI and Hd1 remained the same. These results indicate that OsMADS51 is a flowering promoter, particularly in SDs, and that this gene functions upstream of Ehd1, OsMADS14, and Hd3a. To further investigate the relationship with other flowering promoters, we generated transgenic plants in which expression of Ehd1 or OsGI was suppressed. In Ehd1 RNA interference plants, OsMADS51 expression was not affected, supporting our conclusion that the MADS-box gene functions upstream of Ehd1. However, in OsGI antisense plants, the OsMADS51 transcript level was reduced. In addition, the circadian expression pattern for this MADS-box gene was similar to that for OsGI. These results demonstrate that OsMADS51 functions downstream of OsGI. In summary, OsMADS51 is a novel flowering promoter that transmits a SD promotion signal from OsGI to Ehd1.