bluuebunny/crossref_metadata_2025 huggingface dataset:
Management of Inpatients Colonized or Infected With Antimicrobial-Resistant Bacteria in Hospitals in the United States
Authors: Sunenshine Rebecca H. , Liedtke Laura A. , Fridkin Scott K. , Strausbaugh Larry J. ,   The Infectious Diseases Society of America Emerging Infections Network
Published: April 2006

Background:

Although guidelines for multidrug-resistant organisms generally include recommendations for contact precautions and surveillance cultures, it is not known how frequently U.S. hospitals implement these measures on a routine basis and whether infectious diseases consultants endorse their use.

Methods:

The Emerging Infections Network surveyed its members, infectious diseases consultants, to assess their use of and support for contact precautions and surveillance cultures for routine management of multidrug-resistant organisms in their principal inpatient workplace. Specifically, members were asked about use of these strategies for methicillin-resistantStaphylococcus aureus, vancomycin-resistant enterococci, and multidrug-resistant, gram-negative bacilli on general wards, ICUs, and transplant units.

Results:

Overall, 400 (86%) of 463 respondents supported the routine use of contact precautions to control one or more multidrug-resistant organisms in at least one unit, and 89% worked in hospitals that use them. In contrast, 50% of respondents favored routine use of surveillance cultures to manage at least one multidrug-resistant organism in any unit, and 30% of respondents worked in hospitals that use them routinely in any unit. Members favored routine use of surveillance cultures significantly more in ICUs and transplant units than in general wards for each multidrug-resistant organism (P<.001).

Conclusions:

Most of the infectious diseases consultants endorsed the use of contact precautions for routine management of patients colonized or infected with multidrug-resistant organisms and work in hospitals that have implemented them. In contrast, infectious diseases consultants are divided about the role of routine surveillance cultures in multidrug-resistant organism management, and few work in hospitals that use them.
The Impact of Methicillin Resistance in Staphylococcus aureus Bacteremia on Patient Outcomes: Mortality, Length of Stay, and Hospital Charges
Authors: Cosgrove Sara E. , Qi Youlin , Kaye Keith S. , Harbarth Stephan , Karchmer Adolf W. , Carmeli Yehuda
Published: April 2006

Objective:

To evaluate the impact of methicillin resistance in Staphylococcus aureus on mortality, length of hospitalization, and hospital charges.

Design:

A cohort study of patients admitted to the hospital between July 1, 1997, and June 1, 2000, who had clinically significant S. aureus bloodstream infections.

Setting:

A 630-bed, urban, tertiary-care teaching hospital in Boston, Massachusetts.

Patients:

Three hundred forty-eight patients with S. aureus bacteremia were studied; 96 patients had methicillin-resistant S. aureus (MRSA). Patients with methicillin-susceptible S. aureus (MSSA) and MRSA were similar regarding gender, percentage of nosocomial acquisition, length of hospitalization, ICU admission, and surgery before S. aureus bacteremia. They differed regarding age, comorbidities, and illness severity score.

Results:

Similar numbers of MRSA and MSSA patients died (22.9% vs 19.8%; P = .53). Both the median length of hospitalization after S. aureus bacteremia for patients who survived and the median hospital charges after S. aureus bacteremia were significantly increased in MRSA patients (7 vs 9 days, P = .045; $19,212 vs $26,424, P = .008). After multivariable analysis, compared with MSSA bacteremia, MRSA bacteremia remained associated with increased length of hospitalization (1.29 fold; P = .016) and hospital charges (1.36 fold; P = .017). MRSA bacteremia had a median attributable length of stay of 2 days and a median attributable hospital charge of $6,916.

Conclusion:

Methicillin resistance in S. aureus bacteremia is associated with significant increases in length of hospitalization and hospital charges.
Dispersal ofStaphylococcus aureusInto the Air Associated With a Rhinovirus Infection
Authors: Bassetti Stefano , Bischoff Werner E. , Walter Mark , Bassetti-Wyss Barbara A. , Mason Lori , Reboussin Beth A. , D'Agostino Ralph B. , Gwaltney Jack M. , Pfaller Michael A. , Sherertz Robert J.
Published: April 2006

Objective:

To determine whether healthy adult nasal carriers ofStaphylococcus aureuscan disperseS. aureusinto the air after rhinovirus infection.

Design:

We investigated the “cloud” phenomenon among adult nasal carriers ofS. aureusexperimentally infected with a rhinovirus. Eleven volunteers were studied for 16 days in an airtight chamber wearing street clothes, sterile garb, or sterile garb plus surgical mask; rhinovirus inoculation occurred on day 2. Daily quantitative air, nasal, and skin cultures forS. aureus; cold symptom assessment; and nasal rhinovirus cultures were performed.

Setting:

Wake Forest University School of Medicine, Winston-Salem, North Carolina.

Participants:

Wake Forest University undergraduate or graduate students who had persistent nasal carriage ofS. aureusfor 4 or 8 weeks.

Results:

After rhinovirus inoculation, dispersal ofS. aureusinto the air increased 2-fold with peak increases up to 34-fold. Independent predictors ofS. aureusdispersal included the time period after rhinovirus infection and wearing street clothes (P< .05). Wearing barrier garb but not a mask decreased dispersal ofS. aureusinto the air (P< .05).

Conclusion:

Virus-induced dispersal ofS. aureusinto the air may have an important role in the transmission ofS. aureusand other bacteria.
Public Disclosure of Healthcare-Associated Infections: The Role of the Society for Healthcare Epidemiology of America
Authors: Wong Edward S. , Rupp Mark E. , Mermel Leonard , Perl Trish M. , Bradley Suzanne , Ramsey Keith M. , Ostrowsky Belinda , Valenti August J. , Jernigan John A. , Voss Andreas , Tapper Michael L.
Published: April 2006

Prior to 2004, only two states, Pennsylvania and Illinois, had enacted legislation requiring healthcare facilities to collect nosocomial or healthcare-associated infection (HAI) data intended for public disclosure. In 2004, two additional states, Missouri and Florida, passed disclosure laws. Currently, several other states are considering similar legislation. In California, Senate Bill 1487 requiring hospitals to collect HAI data and report them to the Office of Statewide Health Planning was passed by the legislature, but was not signed into law by Governor Schwarzenegger, effectively vetoing it. The impetus for these laws is complex. Support comes from consumer advocates, who argue that the public has the right to be informed, and from others who view HAI as preventable and hope that public disclosure would provide an incentive to healthcare providers and institutions to improve their care.
An Outbreak of Methicillin-ResistantStaphylococcus aureusSurgical-Site Infections Initiated by a Healthcare Worker With Chronic Sinusitis
Authors: Faibis Frederic , Laporte Cedric , Fiacre Alain , Delisse Chantal , Lina Gerard , Demachy Marie-Claude , Botterel Françoise
Published: April 2006

An investigation was performed following two methicillin-resistantStaphylococcus aureussurgical-site infections in a 946-bed French general hospital. The investigation revealed that the outbreak involved 7 patients in 2 surgical wards and that infections were probably contracted in the operating theater from a healthcare worker suffering from chronic sinusitis.
Persistence of Fluoroquinolone-Resistant, Multidrug-ResistantStreptococcus pneumoniaein a Long-Term–Care Facility Efforts to Reduce Intrafacility Transmission
Authors: Fry Alicia M. , Udeagu Chi Chi N. , Soriano-Gabarro Montse , Fridkin Scott , Musinski Diana , LaClaire Leslie , Elliott John , Cook Debra J. P. , Kornblum John , Layton Marcelle , Whitney Cynthia G.
Published: April 2006

Objective:

We describe an effort to reduce transmission of a multidrug-resistantStreptococcus pneumoniae(MDRSP) in a long-term-care facility (LTCF).

Design:

Longitudinal cross-sectional study.

Setting:

An LTCF in New York City with ongoing disease due to an MDRSP strain among residents with AIDS since a 1995 outbreak. The MDRSP outbreak strain was susceptible to vancomycin but not to other antimicrobials tested, including fluoroquinolones.

Participants:

Residents and staff members of the LTCF during 1999 through 2001.

Intervention:

Implementing standard infection control measures, and developing and implementing "enhanced standard" infection control measures, modified respiratory droplet prevention measures to reduce inter-resident transmission.

Results:

Before the intervention, nasopharyngeal carriage of the MDRSP outbreak strain was detected in residents with AIDS and residents with tracheostomies who were not dependent on mechanical ventilation. The prevalence of nasopharyngeal carriage of the MDRSP outbreak strain was 7.8% among residents who had AIDS and 14.6% among residents with tracheostomies. After training sessions on standard and enhanced standard infection control measures, the staff appeared to have good knowledge and practice of the infection control measures. After the intervention, new transmission among residents with tracheostomies was prevented; however, these residents were prone to persistent tracheal carriage and needed ongoing enhanced standard infection control measures. Ongoing transmission among residents with AIDS, a socially active group, was documented, although fewer cases of disease due to the outbreak strain occurred.

Conclusions:

Infection control contributed to less transmission of MDRSP in the LTCF. Additional strategies are needed to reduce transmission and carriage among certain resident populations.
Compliance with Hand Hygiene and Glove Use in a University-Affiliated Hospital
Authors: Kuzu Nevin , Özer Fadime , Aydemir Semra , Yalcin Ata Nevzat , Zencir Mehmet
Published: April 2006

Objective:

The hands of healthcare workers often transmit pathogens causing nosocomial infections. This study examined compliance with handwashing and glove use.

Setting:

A university-affiliated hospital.

Design:

Compliance was observed covertly. Healthcare workers' demographics, hand hygiene facilities, indications for hand hygiene, compliance with handwashing and glove use in each procedure, and duration of handwashing were recorded.

Results:

Nine nurses and 33 assistant physicians were monitored during the study. One researcher recorded 1,400 potential opportunities for handwashing during 15-minute observation periods. The mean duration of handwashing was 10 + 2 seconds. Most healthcare workers (99.3%) used liquid soap during handwashing, but 79.8% did not dry their hands. For all indications, compliance with handwashing was 31.9% and compliance with glove use was 58.8%. Compliance with handwashing varied inversely with both the number of indications for hand hygiene and the number of patient beds in the hospital room. Compliance with handwashing was better in dirty high-risk situations.

Conclusion:

Compliance with handwashing was low, suggesting the need for new motivational strategies such as supplying feedback regarding compliance rates.
Influence of Matching for Exposure Time on Estimates of Attributable Mortality Caused by Nosocomial Bacteremia in Critically Ill Patients
Authors: Blot Stijn , De Bacquer Dirk , Hoste Eric , Depuydt Pieter , Vandewoude Koenraad , De Waele Jan , Benoit Dominique , De Schuijmer Johan , Colardyn Francis , Vogelaers Dirk
Published: April 2006

Objective:

To evaluate the influence of matching on exposure time on estimates of attributable mortality of nosocomial bacteremia as assessed by matched cohort studies.

Design:

Two retrospective, pairwise-matched (1:2) cohort studies.

Setting:

A 54-bed intensive care unit (ICU) in a university hospital.

Patients:

Patients with nosocomial Escherichia coli bacteremia (n = 68) and control-patients without nosocomial bacteremia (n = 136 for each matched cohort study).

Intervention:

In both matched cohort studies, the same set of bacteremic patients was matched with control-patients using the APACHE II system. In the first study, control-patients were required to have an ICU stay at least as long as the respective bacteremic patient prior to onset of bacteremia (matching on exposure time). In the second study, control-patients were required to have an ICU stay shorter than the stay prior to the development of bacteremia in the respective bacteremic patient (no matching on exposure time).

Results:

For bacteremic patients, the mean ICU stay before onset of the bacteremia was 9 days (median, 6 days). In the first matched cohort study, hospital mortality was not different between bacteremic patients and control-patients (44.1% vs 43.4%; P = .999). In the second study, mortality of bacteremic patients and control-patients was also not different (44.1% vs 47.8%; P = .657). Mortality rates between control groups were not different (43.4% vs 47.8%; P = .543).

Conclusion:

Matching or not matching on exposure time did not alter the estimate of attributable mortality for ICU patients with E. coli bacteremia.
Assessment of the Value of Repeated Point-Prevalence Surveys for Analyzing the Trend in Nosocomial Infections
Authors: Sartor Catherine , Delchambre Anne , Pascal Laurence , Drancourt Michel , De Micco Philippe , Sambuc Roland
Published: April 2006

Objective:

To assess the value of repeated point-prevalence surveys in measuring the trend in nosocomial infections after adjustment for case mix.

Setting:

A 3,500-bed teaching facility composed of 4 acute care hospitals.

Methods:

From May 1992 to June 1996, eight point-prevalence surveys of nosocomial infections were performed in the hospitals using a sampling process. The trend of adjusted nosocomial infection rates was studied for the four surveys that collected data on indwelling catheters. Adjusted rates were calculated using a logistic regression model and a direct standardization method.

Results:

From 1992 to 1996, a total of 20,238 patients were included in the 8 point-prevalence surveys. The nosocomial infection rate decreased from 8.6% in 1992 to 5% in 1996 (P< .001). The analysis of adjusted nosocomial infection rates included 9,600 patients. Four independent risk factors were identified; length of stay greater than 12 days, hospitalization in an intensive care unit, presence of an indwelling urinary catheter, and history of a surgical procedure. After adjustment for case mix, the nosocomial infection rate still showed a downward trend (from 7.2% in 1993 to 5.1% in 1996;P= .02).

Conclusion:

Adjusted prevalence rates of nosocomial infections showed a significant downward trend during the period of this study.
The Wound Care Team: A New Source of Group A Streptococcal Nosocomial Transmission
Authors: Felkner Marilyn , Pascoe Neil , Shupe-Ricksecker Kathleen , Goodman Edward
Published: April 2006

Background:

In August 2001, the Centers for Disease Control and Prevention (CDC) notified the Texas Department of Health (TDH) of an unusually high number of wounds infected with group A streptococci (GAS) in an acute care facility. The TDH initiated an investigation, ultimately identifying 28 cases of non-pharyngeal, non-community-acquired GAS that had occurred between December 2000 and August 2001 and resulted in 3 deaths and 4 nonfatal cases of invasive disease. Ten specimens were sent to the CDC foremmtyping; all isolates wereemmtype 114. However, the source of the outbreak could not be confirmed through laboratory testing at that time.

Methods:

A case–control study was conducted comparing the 10 case-patients with 52 control-patients with wounds that were not infected with GAS. Age, gender, type of wound, underlying medical conditions, and treatment by the wound care team were examined for association with GAS infection.

Results:

The odds of having wound care team treatment versus not having it were 424.2 (95% confidence interval, 19.0 to 9,495.2) among case-patients when compared with control-patients. No other risk factor showed this magnitude of association.

Conclusions:

This study provided overwhelming epidemiologic evidence that the wound care team was the means of transmission. One year later, when two patients receiving wound care were concurrently diagnosed as having GAS, a member of the wound care team was found to be GAS positive for the matchingemmtype. This is the first report of a GAS hospital outbreak linked to a wound care team.
Surgical-Site Infection After Cardiac Surgery: Incidence, Microbiology, and risk Factors
Authors: Lepelletier Didier , Perron Stéphanie , Bizouarn Philippe , Caillon Jocelyne , Drugeon Henri , Michaud Jean-Luc , Duveau Daniel
Published: April 2006

Objective:

To identify risk factors associated with surgical-site infection according to the depth of infection, the cardiac procedure, and the National Nosocomial Infections Surveillance System risk index.

Design:

Prospective survey conducted during a 12-month period.

Setting:

A 48-bed cardiac surgical department in a teaching hospital.

Patients:

Patients admitted for cardiac surgery between February 2002 and January 2003.

Results:

Surgical-site infections were diagnosed in 3% of the patients (38 of 1,268). Of the 38 surgical-site infections, 20 were superficial incisional infections and 18 were mediastinitis for incidence rates of 1.6% and 1.4%, respectively. Cultures were positive in 28 cases and the most commonly isolated pathogen wasStaphylococcus. A National Nosocomial Infections Surveillance System risk index score of 2 or greater was associated with a risk of surgical-site infection (relative risk, 2.4;P< .004). Heart transplantation, mechanical circulatory assistance, coronary artery bypass graft with the use of internal mammary artery, and reoperation for cardiac tamponade or pericard effusion were independent risk factors associated with surgical-site infection.

Conclusions:

Data surveillance using incidence rates stratified by cardiac procedure and type of infection is relevant to improving infection control efforts. Risk factors in patients who developed superficial infection were different from those in patients who developed mediastinitis. Coronary artery bypass graft using internal mammary artery was associated with a high risk of surgical-site infection, and independent factors such as reoperation for cardiac tamponade or pericard effusion increased the risk of infection.
Colonization Status and Appropriate Antibiotic Therapy for Nosocomial Bacteremia Caused by Antibiotic-Resistant Gram-Negative Bacteria in an Intensive Care Unit
Authors: Blot Stijn , Depuydt Pieter , Vogelaers Dirk , Decruyenaere Johan , Waele Jan De , Hoste Eric , Peleman Renaat , Claeys Geert , Verschraegen Gerda , Colardyn Francis , Vandewoude Koenraad
Published: April 2006

Objective:

Timely initiation of antibiotic therapy is crucial for severe infection. Appropriate antibiotic therapy is often delayed for nosocomial infections caused by antibiotic-resistant bacteria. The relationship between knowledge of colonization caused by antibiotic-resistant gram-negative bacteria (ABR-GNB) and rate of appropriate initial antibiotic therapy for subsequent bacteremia was evaluated.

Design:

Retrospective cohort study.

Setting:

Fifty-four-bed intensive care unit (ICU) of a university hospital. In this unit, colonization surveillance is performed through routine site-specific surveillance cultures (urine, mouth, trachea, and anus). Additional cultures are performed when presumed clinically relevant.

Patients:

ICU patients with nosocomial bacteremia caused by ABR-GNB.

Results:

Infectious and microbiological characteristics and rates of appropriate antibiotic therapy were compared between patients with and without colonization prior to bacteremia. Prior colonization was defined as the presence (detected ≥ 2 days before the onset of bacteremia) of the same ABR-GNB in colonization and subsequent blood cultures. During the study period, 157 episodes of bacteremia caused by ABR-GNB were suitable for evaluation. One hundred seventeen episodes of bacteremia (74.5%) were preceded by colonization. Appropriate empiric antibiotic therapy (started within 24 hours) was administered for 74.4% of these episodes versus 55.0% of the episodes that occurred without prior colonization. Appropriate therapy was administered within 48 hours for all episodes preceded by colonization versus 90.0% of episodes without prior colonization.

Conclusion:

Knowledge of colonization status prior to infection is associated with higher rates of appropriate therapy for patients with bacteremia caused by ABR-GNB (Infect Control Hosp Epidemiol 2005;26:575-579).
Tetrasodium EDTA as a Novel Central Venous Catheter Lock Solution Against Biofilm
Authors: Percival Steven L. , Kite Peter , Eastwood Kerrie , Murga Ricardo , Carr Janice , Arduino Matthew J. , Donlan Rodney M.
Published: April 2006

Background:

Central venous catheter (CVC)-related bloodstream infections (BSIs) are known to increase rates of morbidity and mortality in both inpatients and outpatients, including hematology-oncology patients and those undergoing hemodialysis or home infusion therapy. Biofilm-associated organisms on the lumens of these catheters have reduced susceptibility to antimicrobial chemotherapy. This study tested the efficacy of tetrasodium EDTA as a catheter lock solution on biofilms of several clinically relevant microorganisms.

Methods:

Biofilms ofStaphylococcus epidermidis, methicillin-resistantS. aureus, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, andCandida albicanswere grown to levels of approximately 1 × 105colony-forming units (CFU)/cm−1on CVC segments in a model system, then subjected to the tetrasodium EDTA lock treatment.

Results:

Comparisons of biofilms before and after exposure to the 40-mg/mL−1tetrasodium EDTA lock for 21 hours showed that the biofilm viable cell counts of all organisms tested were significantly reduced (P< .05) after exposure to the treatment.

Conclusion:

Antimicrobial lock treatment using 40 mg/mL−1of tetrasodium EDTA for at least 21 hours could significantly reduce or potentially eradicate CVC-associated bio-films of clinically relevant microorganisms (Infect Control Hosp Epidemiol2005;26:515-519).
Why Is It That Internists Do Not Follow Guidelines for Preventing Intravascular Catheter Infections?
Authors: Rubinson Lewis , Wu Albert W. , Haponik Edward F. , Diette Gregory B.
Published: April 2006

Background and Objective:

High morbidity of CVC-related infections has led to national guidelines for their prevention. Despite recommendations for the use of maximal barrier precautions (mask, sterile gloves, gown, and large drape) and skin antisepsis with 2% Chlorhexidine gluconate during CVC insertion, internists in the United States are not implementing these practices frequently. This study sought to identify and characterize the obstacles to and potential opportunities for improving adherence.

Design:

Cross-sectional survey.

Participants:

One thousand randomly selected physician-members of the American College of Physicians-American Society of Internal Medicine.

Methods:

Several potential determinants of adherence to maximal barrier precautions were assessed, including awareness of, agreement with, and ability to implement the recommendation, as well as the practice and training characteristics of the respondents. Factors influencing antiseptic selection were also recorded.

Results:

Of 526 respondents, 178 (34%) had recently inserted CVCs. Clinician experience and subspecialty, awareness of CDC guidelines, and external influences (eg, time to collect equipment) did not affect maximal barrier precautions adherence. The only independent predictor of adherence was high outcome expectancy for the use of large sterile drapes (OR, 5.3; CI95, 2.2-12.6). Availability had the greatest influence on internists' selection of specific antiseptic agents, whereas cost was the least important determinant.

Conclusions:

Despite established efficacy, use of maximal barrier precautions and Chlorhexidine gluconate is low among internists. Because improved adherence to these practices will require increased outcome expectancy for maximal barrier precautions and availability of Chlorhexidine gluconate, targeting these areas through focused education and systems modifications is essential (Infect Control Hosp Epidemiol2005;26:525-533).
Excess Mortality, Hospital Stay, and Cost Due to Candidemia: A Case-Control Study Using Data From Population-Based Candidemia Surveillance
Authors: Morgan Juliette , Meltzer Martin I. , Plikaytis Brian D. , Sofair Andre N. , Huie-White Sharon , Wilcox Steven , Harrison Lee H. , Seaberg Eric C. , Hajjeh Rana A. , Teutsch Steven M.
Published: April 2006

Objective:

To determine the mortality, hospital stay, and total hospital charges and cost of hospitalization attributable to candidemia by comparing patients with candidemia with control-patients who have otherwise similar illnesses. Prior studies lack broad patient and hospital representation or cost-related information that accurately reflects current medical practices.

Design:

Our case-control study included case-patients with candidemia and their cost-related data, ascertained from laboratory-based candidemia surveillance conducted among all residents of Connecticut and Baltimore and Baltimore County, Maryland, during 1998 to 2000. Control-patients were matched on age, hospital type, admission year, discharge diagnoses, and duration of hospitalization prior to candidemia onset.

Results:

We identified 214 and 529 sets of matched case-patients and control-patients from the two locations, respectively. Mortality attributable to candidemia ranged between 19% and 24%. On multivariable analysis, candidemia was associated with mortality (OR, 5.3 for Connecticut and 8.5 for Baltimore and Baltimore County;P< .05), whereas receiving adequate treatment was protective (OR, 0.5 and 0.4 for the two locations, respectively;P< .05). Candidemia itself did not increase the total hospital charges and cost of hospitalization; when treatment status was accounted for, having received adequate treatment for candidemia significantly increased the total hospital charges and cost of hospitalization ($6,000 to $29,000 and $3,000 to $22,000, respectively) and the length of stay (3 to 13 days).

Conclusion:

Our findings underscore the burden of candidemia, particularly regarding the risk of death, length of hospitalization, and cost associated with treatment (Infect Control Hosp Epidemiol2005;26:540-547).
Dynamics of Hemodialysis Catheter Colonization by Coagulase-Negative Staphylococci
Authors: Fux Christoph A. , Uehlinger Dominik , Bodmer Thomas , Droz Sara , Zellweger Claudine , Mühlemann Kathrin
Published: April 2006

Objectives:

Catheter colonization is a necessary but poorly characterized step in the pathogenesis of catheter-related infections. Colonization dynamics of central venous hemodialysis catheters were studied with emphasis on coagulase-negative staphylococci (CoNS) and their population genetics, antibiotic resistance, and biofilm formation. The homogeneity of CoNS colony morphotypes was evaluated.

Design:

Prospective, longitudinal study during 1,158 catheter-days with microbiological analysis of skin swabs, weekly catheter blood and brush samples, and catheter tips.

Setting:

Hemodialysis unit of a university hospital.

Patients:

Twenty-six patients with 24 non-tunneled and 5 tunneled catheters.

Results:

Nineteen (65.5%) of the catheters became colonized, 17 by CoNS. CoNS colonization of the inner lumen was observed in 17.2% of the catheters and was first detectable after 3 weeks. Colonization of the outer surface occurred in 44.8% of the catheters within a minimum of 2 weeks. PFGE of 53 CoNS revealed 10 clones and 20 unique isolates. Isolates from clones were more frequent in catheter blood and brush cultures than were unique isolates (41% vs 15%), were resistant to more antibiotics (median, 7 vs 2), and tended to more often carry theicaAgene (64.1% vs 40%). Four (23.5%) of the catheters showed colonization with a mixture of CoNS based on PFGE. The time from catheter insertion to such mixed CoNS colonization was longer than that for colonization with one CoNS PFGE pattern only (42 vs 25 days).

Conclusions:

Colonization of hemodialysis catheters is dominated by multidrug-resistant,icaA-positive CoNS clones. Mixed CoNS colonization occurs, but is delayed, suggesting a process of sequential superinfection (Infect Control Hosp Epidemiol2005;26:567-574).
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules
Authors: Zhu Shanfeng , Udaka Keiko , Sidney John , Sette Alessandro , Aoki-Kinoshita Kiyoko F. , Mamitsuka Hiroshi
Published: April 2006

Motivation: Various computational methods have been proposed to tackle the problem of predicting the peptide binding ability for a specific MHC molecule. These methods are based on known binding peptide sequences. However, current available peptide databases do not have very abundant amounts of examples and are highly redundant. Existing studies show that MHC molecules can be classified into supertypes in terms of peptide-binding specificities. Therefore, we first give a method for reducing the redundancy in a given dataset based on information entropy, then present a novel approach for prediction by learning a predictive model from a dataset of binders for not only the molecule of interest but also for other MHC molecules.

Results: We experimented on the HLA-A family with the binding nonamers of A1 supertype (HLA-A*0101, A*2601, A*2902, A*3002), A2 supertype (A*0201, A*0202, A*0203, A*0206, A*6802), A3 supertype (A*0301, A*1101, A*3101, A*3301, A*6801) and A24 supertype (A*2301 and A*2402), whose data were collected from six publicly available peptide databases and two private sources. The results show that our approach significantly improves the prediction accuracy of peptides that bind a specific HLA molecule when we combine binding data of HLA molecules in the same supertype. Our approach can thus be used to help find new binders for MHC molecules.

Contact:  mami@kuicr.kyoto-u.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.
FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster
Authors: Adryan Boris , Teichmann Sarah A.
Published: April 2006

Summary: We present a manually annotated catalogue of site-specific transcription factors (TFs) in the fruit fly Drosophila melanogaster. These were identified from a list of candidate proteins with transcription-related Gene Ontology (Go) annotation as well as structural DNA-binding domain assignments. For all 1052 candidate proteins, a defined set of rules was applied to classify information from the literature and computational data sources with respect to both DNA-binding and transcriptional regulatory properties. We propose a set of 753 TFs in the fruit fly, of which 23 are confident novel predictions of this function for previously uncharacterized proteins.

Availability:  

Contact:  boris@mrc-lmb.cam.ac.uk

Supplementary information: Supplementary data are available at
Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment
Authors: Chu K. H. , Li C. P. , Qi J.
Published: April 2006

Motivation: We explored the feasibility of using unaligned rRNA gene sequences as DNA barcodes, based on correlation analysis of composition vectors (CVs) derived from nucleotide strings. We tested this method with seven rRNA (including 12, 16, 18, 26 and 28S) datasets from a wide variety of organisms (from archaea to tetrapods) at taxonomic levels ranging from class to species.

Result: Our results indicate that grouping of taxa based on CV analysis is always in good agreement with the phylogenetic trees generated by traditional approaches, although in some cases the relationships among the higher systemic groups may differ. The effectiveness of our analysis might be related to the length and divergence among sequences in a dataset. Nevertheless, the correct grouping of sequences and accurate assignment of unknown taxa make our analysis a reliable and convenient approach in analyzing unaligned sequence datasets of various rRNAs for barcoding purposes.

Availability: The newly designed software (CVTree 1.0) is publicly available at the Composition Vector Tree (CVTree) web server

Contact:  kahouchu@cuhk.edu.hk
Accounting for elite indoor 200 m sprint results
Authors: Usherwood James R , Wilson Alan M
Published: April 2006

Times for indoor 200 m sprint races are notably worse than those for outdoor races. In addition, there is a considerable bias against competitors drawn in inside lanes (with smaller bend radii). Centripetal acceleration requirements increase average forces during sprinting around bends. These increased forces can be modulated by changes in duty factor (the proportion of stride the limb is in contact with the ground). If duty factor is increased to keep limb forces constant, and protraction time and distance travelled during stance are unchanging, bend-running speeds are reduced. Here, we use results from the 2004 Olympics and World Indoor Championships to show quantitatively that the decreased performances in indoor competition, and the bias by lane number, are consistent with this ‘constant limb force’ hypothesis. Even elite athletes appear constrained by limb forces.
Rapid evolution of sessility in an endemic species flock of the freshwater bivalve
Corbicula
from ancient lakes on Sulawesi, Indonesia
Authors: von Rintelen Thomas , Glaubrecht Matthias
Published: April 2006

The fauna of ancient lakes frequently contains taxa with highly derived morphologies that resulted from
in situ
radiation of lacustrine lineages with high antiquity. We employed a molecular mtDNA phylogeny to investigate this claim for corbiculid freshwater bivalves in two ancient lake systems on the Indonesian island Sulawesi. Among the otherwise mobile corbiculid species flock, only one taxon,
Posostrea anomioides
, in the ancient Lake Poso exhibits a unique habit, i.e. cementing one valve to the substrate. Our data show that
Corbicula
on Sulawesi is polyphyletic, with the endemic riverine taxa in terminal position, and the lacustrine species flock being paraphyletic. Surprisingly,
Posostrea
is not confirmed as a genus distinct from
Corbicula
and genetic distances suggest a rather recent origin from the only other corbiculid species endemic to Lake Poso, the non-cementing
Corbicula possoensis
. While the cementing
anomioides
, despite its unique behavioural and morphological characteristics, clusters together with non-sessile
Corbicula
species, the latter exhibit strong genetic distances in the absence of morphological disparity and fall into several genetically rather distinct clades. These findings suggest that developmental plasticity of animals in ancient lakes rather than the antiquity of lineages might account for the unique morphology of some species.
Effect of growth compensation on subsequent physical fitness in green swordtailsXiphophorus helleri
Authors: Royle Nick J , Lindström Jan , Metcalfe Neil B
Published: April 2006

Early environmental conditions have been suggested to influence subsequent locomotor performance in a range of species, but most measurements have been of initial (baseline) performance. By manipulating early growth trajectories in green swordtail fish, we show that males that underwent compensatory growth as juveniles had a similar baseline swimming endurance when mature adults toad libitumfed controls. However, they had a reduced capacity to increase endurance with training, which is more likely to relate to Darwinian fitness. Compensatory growth may thus result in important locomotor costs later in life.
Physiological constraints on organismal response to global warming: mechanistic insights from clinally varying populations and implications for assessing endangerment
Authors: Bernardo Joseph , Spotila James R
Published: April 2006

Recent syntheses indicate that global warming affects diverse biological processes, but also highlight the potential for some species to adapt behaviourally or evolutionarily to rapid climate change. Far less attention has addressed the alternative, that organisms lacking this ability may face extinction, a fate projected to befall one-quarter of global biodiversity. This conclusion is controversial, in part because there exist few mechanistic studies that show how climate change could precipitate extinction. We provide a concrete, mechanistic example of warming as a stressor of organisms that are closely adapted to cool climates from a comparative analysis of organismal tolerance among clinally varying populations along a natural thermal gradient. We found that two montane salamanders exhibit significant metabolic depression at temperatures within the natural thermal range experienced by low and middle elevation populations. Moreover, the magnitude of depression was inversely related to native elevation, suggesting that low elevation populations are already living near the limit of their physiological tolerances. If this finding generally applies to other montane specialists, the prognosis for biodiversity loss in typically diverse montane systems is sobering. We propose that indices of warming-induced stress tolerance may provide a critical new tool for quantitative assessments of endangerment due to anthropogenic climate change across diverse species.
Long-term sex reversal by oestradiol in amniotes with heteromorphic sex chromosomes
Authors: Freedberg Steven , Bowden Rachel M , Ewert Michael A , Sengelaub Dale R , Nelson Craig E
Published: April 2006

Oestradiol application during embryonic development reverses the sex of male embryos and results in normal female differentiation in reptiles lacking heteromorphic sex chromosomes, but fails to do so in birds and mammals with heteromorphic sex chromosomes. It is not clear whether the evolution of heteromorphic sex chromosomes in amniotes is accompanied by insensitivity to oestradiol, or if the association between oestradiol insensitivity and heteromorphic sex chromosomes can be attributable to phylogenetic constraints in these taxa. Turtles provide an ideal system to examine the potential relationship between oestradiol insensitivity and sex chromosome heteromorphy, since there are species with heteromorphic sex chromosomes that are closely related to species lacking heteromorphic sex chromosomes. We investigated this relationship by examining the long-term effects of oestradiol-17β application on sex determination in
Staurotypus triporcatus
and
Staurotypus salvinii
, two turtle species with male heterogamety. After raising the turtles in the lab for 3 years, we found follicular and Müllerian duct morphology in oestradiol-treated turtles that was identical to that of untreated females. The lasting sex reversal suggests that the evolutionary transition between systems lacking heteromorphic sex chromosomes and those with heteromorphic sex chromosomes is not constrained by a fundamental mechanistic difference.
Supersonic and subsonic stages of dynamic contact between bodies
Authors: Adda-Bedia M , Llewellyn Smith Stefan G
Published: April 2006

Using an acoustic model for the full elastic problem, the early times of the two-dimensional impact of a disc on a rigid plane, or impact between two identical discs, are analysed. We examine some aspects of wave propagation during the impact process and specify stress distributions near the impact region. Unlike the impact of two spheres for which the quasi-static local contact approach of Hertz is well adapted, a complete dynamical approach is necessary for the dynamic contact of two discs. At short times after impact, we show the existence of supersonic effects and we determine the shape of the corresponding stress waves that travel from the impact region through the unstressed body. During the supersonic phase, the contact region grows faster than the speed of sound and the surface outside the contact region is undisturbed. We then solve the transition from supersonic to subsonic regimes and determine the stress distribution near the impact region. Finally, we discuss some physical implications of these results.
Can a spinning egg really jump?
Authors: Mitsui T , Aihara K , Terayama C , Kobayashi H , Shimomura Y
Published: April 2006

Simultaneous three-way observation of optical, acoustic and electric properties demonstrates a theoretical prediction that a spinning prolate spheroid can spontaneously lose contact with the table in the course of its rising motion when the contact friction is weak and the spin is large enough. The durations of the first loss of contact are measured for various initial spin rates and for three aspect ratios. The measurements show good agreements with numerical simulations. It is also visually shown that a spinning hard-boiled egg can jump.
Scale-free foraging by primates emerges from their interaction with a complex environment
Authors: Boyer Denis , Ramos-Fernández Gabriel , Miramontes Octavio , Mateos José L , Cocho Germinal , Larralde Hernán , Ramos Humberto , Rojas Fernando
Published: April 2006

Scale-free foraging patterns are widespread among animals. These may be the outcome of an optimal searching strategy to find scarce, randomly distributed resources, but a less explored alternative is that this behaviour may result from the interaction of foraging animals with a particular distribution of resources. We introduce a simple foraging model where individual primates follow mental maps and choose their displacements according to a maximum efficiency criterion, in a spatially disordered environment containing many trees with a heterogeneous size distribution. We show that a particular tree-size frequency distribution induces non-Gaussian movement patterns with multiple spatial scales (Lévy walks). These results are consistent with field observations of tree-size variation and spider monkey (Ateles geoffroyi) foraging patterns. We discuss the consequences that our results may have for the patterns of seed dispersal by foraging primates.
Copepods induce paralytic shellfish toxin production in marine dinoflagellates
Authors: Selander Erik , Thor Peter , Toth Gunilla , Pavia Henrik
Published: April 2006

Among the thousands of unicellular phytoplankton species described in the sea, some frequently occurring and bloom-forming marine dinoflagellates are known to produce the potent neurotoxins causing paralytic shellfish poisoning. The natural function of these toxins is not clear, although they have been hypothesized to act as a chemical defence towards grazers. Here, we show that waterborne cues from the copepodAcartia tonsainduce paralytic shellfish toxin (PST) production in the harmful algal bloom-forming dinoflagellateAlexandrium minutum. InducedA. minutumcontained up to 2.5 times more toxins than controls and was more resistant to further copepod grazing. Ingestion of non-toxic alternative prey was not affected by the presence of inducedA. minutum. The ability ofA. minutumto sense and respond to the presence of grazers by increased PST production and increased resistance to grazing may facilitate the formation of harmful algal blooms in the sea.
Sustainable pest regulation in agricultural landscapes: a review on landscape composition, biodiversity and natural pest control
Authors: Bianchi F.J.J.A , Booij C.J.H , Tscharntke T
Published: April 2006

Agricultural intensification has resulted in a simplification of agricultural landscapes by the expansion of agricultural land, enlargement of field size and removal of non-crop habitat. These changes are considered to be an important cause of the rapid decline in farmland biodiversity, with the remaining biodiversity concentrated in field edges and non-crop habitats. The simplification of landscape composition and the decline of biodiversity may affect the functioning of natural pest control because non-crop habitats provide requisites for a broad spectrum of natural enemies, and the exchange of natural enemies between crop and non-crop habitats is likely to be diminished in landscapes dominated by arable cropland. In this review, we test the hypothesis that natural pest control is enhanced in complex patchy landscapes with a high proportion of non-crop habitats as compared to simple large-scale landscapes with little associated non-crop habitat. In 74% and 45% of the studies reviewed, respectively, natural enemy populations were higher and pest pressure lower in complex landscapes versus simple landscapes. Landscape-driven pest suppression may result in lower crop injury, although this has rarely been documented. Enhanced natural enemy activity was associated with herbaceous habitats in 80% of the cases (e.g. fallows, field margins), and somewhat less often with wooded habitats (71%) and landscape patchiness (70%). The similar contributions of these landscape factors suggest that all are equally important in enhancing natural enemy populations. We conclude that diversified landscapes hold most potential for the conservation of biodiversity and sustaining the pest control function.
Electrophysiological diversity of the dorsal raphe cells across the sleep–wake cycle of the rat
Authors: Urbain Nadia , Creamer Katherine , Debonnel Guy
Published: April 2006

Through their widespread projections to the entire brain, dorsal raphe cells participate in many physiological functions and are associated with neuropsychiatric disorders. In previous studies, the width of action potentials was used as a criterion to identify putative serotonergic neurons, and to demonstrate that cells with broad spikes were more active in wakefulness, slowed down their activity in slow wave sleep and became virtually silent during paradoxical sleep. However, recent studies reported that about half of these presumed serotonergic cells were not immunoreactive for tyrosine hydroxylase. Here, we re‐examine the electrophysiological properties of dorsal raphe cells across the sleep–wake cycle in rats by the extracellular recording of a large sample of single units (n= 770). We identified two major types of cells, which differ in spike waveform: a first population characterized by broad, mostly positive spikes, and a second one displaying symmetrical positive–negative spikes with a large distribution of spike durations (0.6–3.2 ms). Although we found classical broad‐spike cells that were more active in wakefulness, we also found that about one‐third of these cells increased or did not change their firing rate during sleep compared with wakefulness. Moreover, 62% of the latter cells were active in paradoxical sleep when most of raphe cells were silent. Such a diversity in the neuronal firing behaviour is important in the light of the recent controversy regarding the neurochemical identity of dorsal raphe cells exhibiting broad spikes. Our results also suggest that the dorsal raphe contains subpopulations of neurons with reciprocal activity across the sleep–wake cycle.