bluuebunny/crossref_metadata_2025_split huggingface dataset:
BioFire FilmArray Decreases Infection Control Isolation Times by 4 days in ICU, BMT and Respiratory Wards
Authors: Wong Titus , Stefanovic Aleksandra , Locher Kerstin , Bryce Elizabeth , Grant Jennifer M , Connolly Eithne , Woznow Tracey , Charles Marthe , Hoang Linda Mn , Jassem Agatha , Roscoe Diane 
Published: October 2017

Abstract

Background
Novel, rapid, syndromic testing of patients presenting with respiratory infections has the potential to improve patient access and care by decreasing time to diagnosis. BioFire FilmArray (BioFire Diagnostics, bioMerieux) is a cartridge-based, multiplex PCR platform capable of detecting 17 viral and 3 bacterial targets in one hour. This study assessed the impact of implementing this technology on the duration of infection control isolation.

Methods
A randomized control trial in a 900-bed tertiary-care academic hospital was conducted between December 2016 and January 2017. Fifty consecutive samples of patients with respiratory infections on our ICU, BMT and Respiratory wards to received either BioFire FilmArray Respiratory Panel (BF) diagnostic testing or our routine diagnostic testing (RO) consisting of an influenza A/B/RSV PCR (in-house) followed by Luminex NxTag Respiratory Pathogen Panel that was batched at a reference lab. Five patient charts with missing data were excluded from analysis. Statistical analysis was completed using RStudio Version 1.0.136 – © 2009–2016 RStudio, Inc.

Results
Patients randomized to the BF arm remained on respiratory isolation precautions on average (42.3 ± 72.9 hours) over 100 hours less than patients randomized to the routine arm (151.3 ± 151.8 hours) (95% CI: 35.6–184.4 hours, P = 0.0052).

Conclusion
Implementing the BioFire FilmArray Respiratory Panel decreased infection control isolation time by approximately 4 days compared with routine testing; further study is warranted to determine the impact of this technology on patient outcomes and cost benefit.

Disclosures
T. Wong, bioMerieux: Investigator, Research grant A. Stefanovic, bioMerieux: Investigator, Research grant E. Bryce, bioMerieux: Investigator, Research grant J. M. Grant, bioMerieux: Investigator, Research grant D. Roscoe, bioMerieux: Investigator, Research grant
When to Order a Respiratory Viral Panel (RVP): Physician Use in Clinical Practice
Authors: Linn Alexandra , Wang Li , Silveira Fernanda P , Williams John V , Zimmerman Richard , Rinaldo Charles R , Michaels Marian 
Published: October 2017

Abstract

Background
Multiplex RVP assays are frequently offered at medical centers to screen for viruses using nucleic acid technology. The University of Pittsburgh Medical Center (UPMC) uses the Genmark eSensor RVP detecting 14 virus types/subtypes. This study evaluated how RVPs are used in a large medical center to better understand physician practices.

Methods
A 32 question, descriptive survey, created using the Qualtrics survey database, was sent via email to pediatric, emergency, internal, and family physicians at large academic hospitals in the UPMC network. The anonymous survey was sent 3 times between January 2017 and March 2017. Survey data were analyzed using the SPSS statistics software.

Results
543/1,265 (43%) survey responses were received; 492 were evaluable. 56% were female; 42% see children, 45% see adults, 13% see both; 16% see patients in the ED. Training levels included 51% residents/fellows and 49% attendings. Of doctors responding, 87% order RVPs. Most (85%) have changed treatment decisions based on a RVP result; 53% changed management ~50% of the time.

Conclusion
Physicians order RVPs most frequently if they believe the results will change treatment. RVPs are ordered more for young and elderly patients, and those with underlying immunosuppression or chronic illness. Cost does not limit physician ordering and most are unaware of it. Suspected influenza or specific virus is also considered.

Disclosures
J. V. Williams, Quidel: Scientific Advisor, Consulting fee GlaxoSmithKline: Scientific Advisor, Consulting fee R. Zimmerman, Sanofi: Grant Investigator, Grant recipient
Sensitivity and Specificity of the Quidel Sofia Influenza A+B FIA Rapid Influenza Detection Test in Long-Term Care Facilities
Authors: Temte Jonathan , Checovich Mary , Barlow Shari , Shult Peter , Reisdorf Erik , Haupt Thomas 
Published: October 2017

Abstract

Background
Influenza is a significant pathogen for long-term care facility (LTCF) residents. As part of a randomized controlled trial to assess early detection of influenza in LTCFs, we deployed rapid influenza detection tests (RIDTs) at intervention LTCFs. Our primary objectives for this interim analysis were to evaluate the sensitivity and specificity of the Quidel Sofia® Influenza A+B Fluorescent Immunoassay RIDT in a high-risk, nontraditional population, and to describe the virology of acute respiratory infections (ARI) in LTCF residents.

Methods
Personnel at LCTFs identified cases of ARI, collected nasal specimens, and ran RIDTs from 10/21/2016 to 4/28/2017. The residual nasal swab and leftover lysis buffer were placed into a viral transport medium tube and sent to the Wisconsin State Laboratory of Hygiene for confirmatory influenza RT-PCR testing. In addition, all specimens were tested for other viruses using the Luminex NxTAG® Respiratory Pathogen Panel. Sensitivity and specificity of the Sofia RIDT were calculated using RT-PCR results as the reference standard.

Results
Specimens were collected from 228 residents (mean age = 71.3 ± 22.4 years). The mean time from symptom onset to specimen collection was 1.4 ± 1.6 days (range: 0-7 days). Respiratory viruses were identified in 134/228 cases (58.8%); influenza viruses (A: 7.5% and B: 14.5%) were the most commonly detected virus by PCR, followed by rhinovirus/enterovirus (13.2%), RSV (11.0%) and coronaviruses (10.1%). The sensitivities of Sofia RIDT for influenza A and influenza B were 77.8% (95% CI: 52.4–93.6%) and 80.0% (95% CI: 61.4–92.3%), respectively, with specificities of 98.4% (95.3–99.7%) and 97.1% (93.4–99.1%), respectively. Overall performance assessment for influenza A or B yielded a sensitivity of 79.2% (65.0–89.5%) and specificity of 96.1% (91.7–98.6%). The estimated likelihood of discovering one of the first two influenza cases at a LTCF using this RIDT is estimated to be ≥95.7%.

Conclusion
Although a wide constellation of respiratory viruses cause ARIs within LTCF populations, influenza is very common. Early ARI recognition in residents, with testing shortly after symptom onset, likely contributed to high performance of the Sofia RIDT. Use of RIDTs allows early identification of influenza with high sensitivity and specificity in elderly LTCF residents.

Disclosures
J. Temte, Quidel: Investigator, Research support
Detection of Cytomegalovirus (CMV) in Saliva of Congenitally Infected Neonates
Authors: Wissel Mark , Demmler Gail , Gandaria Cindy , Cravens Stephanie , Berg Amy , Widen Ashley , Altrich Michelle , Kleiboeker Steve 
Published: October 2017

Abstract

Background
Congenital cytomegalovirus (cCMV) infection is a significant, but potentially under-recognized health threat. Approximately 1 of 150 neonates in the US is born with cCMV infection, with 20% exhibiting long-term health problems due to infection. Both targeted CMV testing of newborns with failed hearing screens and universal CMV screening of all newborns have been proposed as approaches to identify infected newborns early in life. Congenital CMV infection can be diagnosed by testing a newborn’s saliva, urine, or blood by CMV qPCR or culture. Dried blood spots for use in qPCR assays have been shown to be a minimally sensitive specimen. Of the three specimens that are recommended, only saliva is simple, noninvasive and easy to collect.

Methods
In this study, we have validated a real-time (TaqMan) PCR assay for use in testing saliva samples from neonates for the presence of CMV. In conjunction with compatible clinical findings, a CMV positive PCR result forms the basis for a clinical diagnosis. The assay was shown to be specific for CMV, with no cross-reactivity detected for other human herpesviruses or for other human viral pathogens. Since CMV shedding levels from cCMV cases are known to be above the analytical limit of detection for the assay, and samples are collected in a nonsterile environment in which incidental CMV shedding may be present from other neonatal or pediatric patients, the reporting cutoff for this assay was set at 1000 IU/mL. Following analytical validation of the assay, stored (-80°C) residual de-identified clinical saliva samples were tested. The comparator assay was CMV cell culture, and the clinical diagnosis was used to resolve discrepant results.

Results
A total of 9 saliva samples, collected at approx. 1 month of age (or earlier) were tested by both assays. Two samples were negative by both assays and 6 samples were positive by both assays. A single sample was positive by qPCR but negative by cell culture; the qPCR value for this sample was 15,100 IU/mL. This infant had two positive urine cultures, a positive saliva shell vial culture and was clinically confirmed to have cCMV infection.

Conclusion
This study suggests improved sensitivity of qPCR over CMV cell culture for identification of neonates congenitally infected with CMV.

Disclosures
M. Wissel, Viracor Eurofins Laboratories: Employee, Salary S. Cravens, Viracor Eurofins Laboratories: Employee, Salary A. Berg, Viracor Eurofins Laboratories: Employee, Salary A. Widen, Viracor Eurofins Laboratories: Employee, Salary M. Altrich, Viracor Eurofins Laboratories: Employee, Salary S. Kleiboeker, Viracor Eurofins Laboratories: Employee, Salary
CSF HSV PCR Testing in Adults and Children with Meningitis and Encephalitis
Authors: Parra Liliana , Hasbun Rodrigo , Salazar Lucrecia , Aguilera Elizabeth , Wootton Susan 
Published: October 2017

Abstract

Background
Herpes simplex virus (HSV) is a common treatable cause of meningitis and encephalitis. Delayed antiviral therapy is associated with worse clinical outcomes in HSV encephalitis.

Objectives
To determine the utilization of a cerebrospinal fluid (CSF) HSV polymerase chain reaction (PCR) and identify predictors for a positive HSV PCR result.

Methods
A retrospective review of 751 adults and children with meningitis and encephalitis at 9 hospitals in Houston TX from January 1 2005 to December 31 2010.

Results
Of 751 patients, 331 (44%) underwent CSF HSV PCR testing. Adults were more commonly tested than children (84% vs. 69%, P &lt;0.0001). Additionally, patients with more comorbidities and clinical findings of encephalitis (e.g., altered mental status, focal neurological findings, seizures) were more commonly tested for HSV (P &lt;0.001). Patients tested for HSV were also more likely to be evaluated for West Nile Virus, receive empiric acyclovir and have worse outcomes (P &lt; 0.001). In total, 48 of 331 (14.5%) patients tested had a positive CSF HSV PCR. Predictors for a positive CSF HSV PCR on logistic regression analysis were stiff neck (odds ratio [OR], 2.181 [1.090–4.366]; P = 0.028, lymphocytic pleocytosis &gt;50% lymphocytes (OR, 6.187 [1.412–27.11] P = 0.016, and CSF protein &gt; 100mg/dl (OR, 3.279 [1.105–9.731] P = 0.032.

Conclusion
CSF HSV PCR is underutilized in community acquired meningitis and encephalitis and is done more frequently in adults and in those with an encephalitis presentation.

Disclosures
R. Hasbun, Biomeriaux: Consultant, Consulting fee Biofire: Speaker’s Bureau, Speaker honorarium Merck: Speaker’s Bureau, Speaker honorarium Pfizer: Speaker’s Bureau, Speaker honorarium Medicine’s Co: Speaker’s Bureau, Speaker honorarium
The Expression of hsp-miRNA-200b-3p and -200c-3p in Human Cytomegalovirus-infected Formalin-Fixed, Paraffin-Embedded Tissues
Authors: Lee Kyoung Hwa , Min Seoyeon , Yoo Seul Gi , Lim Beom Jin , Jo Jeong-Hyeon , Han Sang Hoon , Song Young Goo 
Published: October 2017

Abstract

Background
Human cytomegalovirus (HCMV), which exist as asymptomatic latent status, can cause the tissue invasive disease through reactivation in various immunocompromised conditions. Hsp-microRNA has a specific function of post transcriptional suppression through binding with 3’ untranslated region (UTR) of mRNA. In previous study, hsp-miR-200b-3p and -200c-3p had high probability of conjugation with 3’UTR of mRNA encoded by HCMV UL 122–123 region, which translate the immediate early protein 2 (IE2) protein. IE2 (pp86) plays an essential role to initiate and regulate viral early (E) gene activation as well as propagate the subsequent steps of HCMV lytic replication. This study was aimed to evaluate whether HCMV-infected tissue had a lower expression level of hsp-miR-200b-3p and -200c-3p.

Methods
We had collected the formalin-fixed, paraffin-embedded tissues (FFPEs) with cytopathic pathologic findings as well as positive immunohistochemical stain (IHC) test for HCMV (N = 111). The HCMV-uninfected normal tissues (N = 77) were selected among FFPEs with neither infection nor inflammation as well as negative HCMV IHC test. We performed TaqMan® MicroRNA real-time RT-PCR to measure the expression levels of hsp-miR-200b-3p and -200c-3p and TaqMan® real-time PCR for HCMV UL83 region to measure HCMV viral load in each FFPE. We utilized the standard curves consisting of mirVanaTM miRNA mimics corresponding to each of two miRNAs, ranging from 106 to 101 copies/µL and HCMV NIBSC 09/162 strain, ranging from 5 X 106 to 5 X 101 IU/mL.

Results
The levels of hsp-miR-200b-3p and -200c-3p were strongly correlated with r=0.844 (P &lt; 0.001). The expressions levels of hsp-miR-200b-3p in HCMV-infected FFPEs (log10 3.50 ± 0.13 copies/µL) were significantly lower than normal tissues (log10 5.24 ± 0.12 copies/µL of input RNA, P &lt; 0.001). Also, HCMV-infected FFPEs were significantly lower levels of hsp-miR-200c-3p compared than normal tissues (log10 5.28 ± 0.18 vs. 7.81 ± 0.11 copies/µL of input RNA, P = 0.025). The levels of miR-200b-3p and -200c-3p had the significant inverse correlation with HCMV VL (200b-3p, spearman r=-0.392, P &lt; 0.001 and 200c-3p, spearman r=-0.355, P &lt; 0.001).

Conclusion
The low expression of hsp-miRNA-200b-3p and -200c-3p could play a pathophysiologic role of development of HCMV tissue-invasive disease.

Disclosures
All authors: No reported disclosures.
Human Adenovirus (HAdV) Viremia in Immunocompetent Children with HAdV Infection in Respiratory Specimens: Does Viremia Predict Severity of Illness?
Authors: Song Eunkyung , Wang Huanyu , Leber Amy , Jaggi Preeti 
Published: October 2017

Abstract

Background
The interpretation of HAdV PCR from upper respiratory tract (RT) specimens can be challenging due to prolonged low grade viral shedding. We hypothesized that HAdV detection in the blood (viremia) is more common in acute HAdV infection with high respiratory viral burden (VB) compared with those with low VB in the RT. We sought to determine the frequency of HAdV viremia in immunocompetent children who have detectable HAdV in the RT.

Methods
We prospectively identified + HAdV in RT specimens from emergency department or inpatients using semi-quantitative real-time PCR (Ct &lt;40) or multiplex respiratory viral PCR (FILMARRAY RESPIRATORY PANEL v1.7) and prospectively collected available whole blood from 8/2013 to 2/2015. Blood was considered positive for HAdV if Ct was &lt;40 in whole blood. We compared virologic, including HAdV type from the RT and blood, and clinical characteristics between viremic and non-viremic groups using Mann–Whitney or chi-square as appropriate.

Results
There were 196 unique patients with + HAdV in RT specimens as well as available blood for PCR (median age=1.3 years old). Blood and RT samples were obtained on the same calendar day in 78% of patients. Among these 196 patients, 163 (83%) were hospitalized and 58 (36%) were admitted to PICU. HAdV was detected in the blood in 33% of patients. Upper respiratory tract infections were more common (P = 0.026) and the duration of fever at the time of enrollment was longer in the viremia group (3 vs. 2 days, P = 0.043). There was no difference in ICU admission between two groups. Coinfections with bacterial pathogens from sterile sites were only found in the non-viremic group (4%); these included S. aureus or pneumococcal bacteremia, E. coli urinary tract infections, or pneumococcal pneumonia. HAdV VB in RT were significantly higher in the viremia group (Ct median 25.01 vs.. 36.38, P &lt; 0.0001). Species C was more predominant in the viremia group compared with non C (A, B/E, D, F) (P = 0.018). RT type was 100% concordant with blood type.

Conclusion
HAdV viremia is relatively common in immunocompetent children with HAdV infection in the RT. Subjects with viremia had significantly higher VB in the RT, but this didn’t seem to be correlated with disease severity. HAdV viremia may be useful tool to add further evidence of acute HAdV infection.

Disclosures
A. Leber, BioFIre Diagnostics: Research Contractor and Scientific Advisor, Research support, Speaker honorarium and Travel expenses
Feasibility and Validation of Viral Respiratory Disease Surveillance in a Combat Theater Using the Filmarray Respiratory Panel
Authors: Maves Ryan , Larson Derek , Dempsey Michael , Connors Benjamin , Baldwin James , Thomas Richard , Starr Clarise 
Published: October 2017

Abstract

Background
Viral respiratory infections are a significant threat to deployed military units. Pathogen-based surveillance may be hampered by limitations in trained personnel in theater, difficulty with specimen shipment, and technical issues with equipment maintenance. In this project, we evaluated the performance of the FilmArray respiratory panel at military clinics in Afghanistan and compare results to testing performed in the United States.

Methods
Participants were recruited after presenting at military clinics at Bagram Airfield (BAF), Afghanistan, in 2013–2014 with fever (≥38° C) and respiratory symptoms (cough, dyspnea, chest pain, and/or sore throat). General medical laboratory staff at BAF were trained to operate the FilmArray; nasopharyngeal swabs were obtained and tested in-theater using the FilmArray respiratory panel (Biofire Diagnostics, Salt Lake City, UT). Samples were then shipped to the USAFSAM Applied Technology Center in 50% RNALater (Qiagen, Valencia, CA) without dry ice and then retested using the same panel. Selected influenza isolates then underwent sequencing to evaluate for potential novel circulating strains.

Results
29 specimens underwent testing. A virus was identified on FilmArray in 22/29 specimens at BAF and 24/29 specimens at USAFSAM, of whom 17/29 had influenza A. Positive results between BAF and USAFSAM were concordant in all cases; 2 of the negative results at BAF were identified as having influenza A and rhinovirus, respectively. Among those with influenza A, all but one had undergone seasonal influenza vaccination. 5 influenza isolates then underwent sequencing; 2 were A(H1N1pdm09) consistent with the predominant 2012–2013 strain, while 3 were A(H3N2) viruses with HA mutations that differed from those in the 2013–2014 vaccine strain. No resistance-associated neuraminidase mutations were identified.

Conclusion
Surveillance using the FilmArray system is effective and feasible in theater by general laboratory staff. H1N1 and H3N2 influenza A viruses predominated in this sample of acute respiratory infections in a deployed military setting despite high vaccination rates. The use of the RNALater preservative is an effective method for specimen transport without requiring a cold chain and may facilitate biosurveillance in remote settings.

Disclosures
All authors: No reported disclosures.
Clinical Predictors of Shigella and Campylobacter Infection in Children in the United States
Authors: Smith Timothy , Ye Xiangyang , Stockmann Chris , Cohen Daniel , Leber Amy , Daly Judy , Jackson Jami , Selvarangan Rangaraj , Kanwar Neena , Bender Jeffery , Bard Jennifer Dien , Festekjian Ara , Duffy Susan , Larsen Chari , Baca Tanya , Holmberg Kristen , Bourzac Kevin , Chapin Kimberle C , Pavia Andrew , Leung Daniel 
Published: October 2017

Abstract

Background
Infectious gastroenteritis is a major cause of morbidity and mortality among children worldwide. While most episodes are self-limiting, for select pathogens such as Shigella and Campylobacter, etiological diagnosis may allow effective antimicrobial therapy and aid public health interventions. Unfortunately, clinical predictors of such pathogens are not well established and are based on small studies using bacterial culture for identification.

Methods
We used prospectively collected data from a multi-center study of pediatric gastroenteritis employing multi-pathogen molecular diagnostics to determine clinical predictors associated with 1) Shigella and 2) Shigella or Campylobacter infection. We used machine learning algorithms for clinical predictor identification, then performed logistic regression on features extracted plus pre-selected variables of interest.

Results
Of 993 children enrolled with acute diarrhea, we detected Shigella spp. in 56 (5.6%) and Campylobacter spp. in 24 (2.4%). Compared with children who had neither pathogen detected (of whom, &gt;70% had ≥1 potential pathogen identified), bloody diarrhea (odds ratio 4.0), headache (OR 2.2), fever (OR 7.1), summer (OR 3.3), and sick contact with GI illness (OR 2.2), were positively associated with Shigella, and out-of-state travel (OR 0.3) and vomiting and/or nausea (OR 0.4) were negatively associated (Table). For Shigella or Campylobacter, predictors were similar but season was no longer significantly associated with infection.

Conclusion
These results can create prediction models and assist clinicians with identifying patients who would benefit from diagnostic testing and earlier antibiotic treatment. This may curtail unnecessary antibiotic use, and help to direct and target appropriate use of stool diagnostics.

Disclosures
A. Leber, BioFIre Diagnostics: Research Contractor and Scientific Advisor, Research support, Speaker honorarium and Travel expenses J. Daly, Biofire: Grant Investigator, Grant recipient R. Selvarangan, BioFire Diagnostics: Board Member and Investigator, Consulting fee and Research grant Luminex Diagnostics: Investigator, Research grant J. Dien Bard, BioFire: Consultant and Investigator, Research grant and Speaker honorarium K. Holmberg, BioFire Diagnostics: Employee, Salary K. Bourzac, BioFire Diagnostics: Employee, Salary K. C. Chapin, BioFire Diagnstics: Investigator, Research support A. Pavia, BioFire Diagnostics: Grant Investigator, Research grant