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Noble BA, Jiudice SS, Jones JD, Timbrook TT. Reemergence of Bordetella parapertussis, United States, 2019-2023. Emerg Infect Dis 2024; 30:1058-1060. [PMID: 38666607 PMCID: PMC11060467 DOI: 10.3201/eid3005.231278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Abstract
To determine changes in Bordetella pertussis and B. parapertussis detection rates, we analyzed 1.43 million respiratory multiplex PCR test results from US facilities from 2019 through mid-2023. From mid-2022 through mid-2023, Bordetella spp. detection increased 8.5-fold; 95% of detections were B. parapertussis. While B. parapertussis rates increased, B. pertussis rates decreased.
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Timbrook TT, Glancey M, Noble BA, Eng S, Heins Z, Hommel B, Tessonneau M, Galvin BW, Macalino G. The epidemiology of pediatric outpatient acute respiratory tract infections in the US: a multi-facility analysis of multiplex PCR testing from 2018 to 2023. Microbiol Spectr 2024; 12:e0342323. [PMID: 38095469 PMCID: PMC10782947 DOI: 10.1128/spectrum.03423-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 11/20/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Post-pandemic, it is essential to understand the epidemiology of pediatric acute respiratory tract infections (ARTIs). Our multi-facility study elucidates the outpatient epidemiology of pediatric ARTI using highly multiplexed PCR testing, providing critical insights into the evolving landscape of the etiological agents with a particular focus on the years following the emergence of SARS-CoV-2. Utilizing data from two different multiplex PCR panels, our research provides a comprehensive analysis of respiratory pathogen positivity from 2018 to 2023. Our findings indicate that over half of the annual test results identified at least one pathogen, primarily of viral origin. Intriguingly, despite the surge in testing during the COVID-19 pandemic, pathogen detection rates remain similar to the pre-pandemic era. These data hold significant implications for directing antimicrobial stewardship strategies, curbing unnecessary antibiotic use in pediatric respiratory diseases, and the value of multiplex PCR testing in the outpatient setting among pediatrics.
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Affiliation(s)
- Tristan T. Timbrook
- Global Medical Affairs, bioMérieux, Salt Lake City, Utah, USA
- Department of Pharmacotherapy, College of Pharmacy, University of Utah, Salt Lake City, Utah, USA
| | | | | | - Stephen Eng
- Baker Tilly US, LLP, New York, New York, USA
| | - Zoe Heins
- Global Medical Affairs, bioMérieux, Salt Lake City, Utah, USA
| | | | - Marie Tessonneau
- Baker Tilly US, LLP, New York, New York, USA
- Global Medical Affairs, bioMérieux, Marcy l'Étoile, France
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Noble BA, Jurcic Smith KL, Jones JD, Galvin BW, Timbrook TT. Candida auris rates in blood culture on the rise: results of US surveillance. Microbiol Spectr 2023; 11:e0221623. [PMID: 37623375 PMCID: PMC10580899 DOI: 10.1128/spectrum.02216-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/12/2023] [Indexed: 08/26/2023] Open
Abstract
Candida auris is an emerging pathogen that poses a significant public health risk. Its multidrug resistance has led to high mortality, making rapid detection crucial for effective treatment and prevention of transmission. Recent data from the Centers for Disease Control and Prevention indicate a substantial increase in C. auris cases in the United States, with a 95% rise in 2021. To provide an update on the detection rates of C. auris, we analyzed blood culture results from a near real-time cloud-based surveillance network, BioFire Trend. From January 2021 to April 2023, 34 C. auris detections were observed. The analysis showed a notable increase in detections in 2023 compared to previous years. The detection rate in 2023 was higher in all four US Census Regions, except for the Northeast, where it remained constant. The findings emphasize the continuous rise in C. auris cases and highlight the importance of near real-time surveillance systems in monitoring this emerging pathogen.
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Affiliation(s)
| | | | - Jay D. Jones
- Data Science, bioMérieux, Salt Lake City, Utah, USA
| | | | - Tristan T. Timbrook
- Global Medical Affairs, bioMérieux, Salt Lake City, Utah, USA
- Department of Pharmacotherapy, University of Utah College of Pharmacy, Salt Lake City, Utah, USA
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Evaluation and Clinical Impact of Biofire FilmArray Pneumonia Panel Plus in ICU-Hospitalized COVID-19 Patients. Diagnostics (Basel) 2022; 12:diagnostics12123134. [PMID: 36553141 PMCID: PMC9777407 DOI: 10.3390/diagnostics12123134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Microbiological diagnosis by using commercial multiplex quantitative PCR systems provides great advantages over the conventional culture. In this work, the Biofire FilmArray Pneumonia Panel Plus (FAPP+) was used to test 144 low respiratory tract samples from 105 COVID-19 patients admitted to an Intensive Care Unit (ICU), detecting 78 pathogens in 59 (41%) samples. The molecular panel was evaluated by using the conventional culture (CC) as comparator, which isolated 42 pathogens in 40 (27.7%) samples. The overall percentage of agreement was 82.6%. Values of sensitivity (93%), specificity (62%), positive predictive value (50%), and negative predictive value (96%) were obtained. The mean time elapsed from sample extraction to modification of antibiotic treatment was 7.6 h. A change in antimicrobial treatment after the FAPP+ results was performed in 27% of patients. The FAPP+ is a highly sensitive diagnostic method that can be used to significantly reduce diagnostic time and that allows an early optimization of antimicrobial treatment.
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Messacar K, Baker RE, Park SW, Nguyen-Tran H, Cataldi JR, Grenfell B. Preparing for uncertainty: endemic paediatric viral illnesses after COVID-19 pandemic disruption. Lancet 2022; 400:1663-1665. [PMID: 35843260 PMCID: PMC9282759 DOI: 10.1016/s0140-6736(22)01277-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 02/06/2023]
Affiliation(s)
- Kevin Messacar
- Department of Pediatrics, Section of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, USA; Children's Hospital Colorado Aurora, CO 80045, USA.
| | - Rachel E Baker
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Hai Nguyen-Tran
- Department of Pediatrics, Section of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jessica R Cataldi
- Department of Pediatrics, Section of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, USA; Children's Hospital Colorado Aurora, CO 80045, USA
| | - Bryan Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA; Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
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Probst V, Spieker AJ, Stopczynski T, Stewart LS, Haddadin Z, Selvarangan R, Harrison CJ, Schuster JE, Staat MA, McNeal M, Weinberg GA, Szilagyi PG, Boom JA, Sahni LC, Piedra PA, Englund JA, Klein EJ, Michaels MG, Williams JV, Campbell AP, Patel M, Gerber SI, Halasa NB. Clinical Presentation and Severity of Adenovirus Detection Alone vs Adenovirus Co-detection With Other Respiratory Viruses in US Children With Acute Respiratory Illness from 2016 to 2018. J Pediatric Infect Dis Soc 2022; 11:430-439. [PMID: 35849119 DOI: 10.1093/jpids/piac066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/28/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Human adenovirus (HAdV) is commonly associated with acute respiratory illnesses (ARI) in children and is also frequently co-detected with other viral pathogens. We compared clinical presentation and outcomes in young children with HAdV detected alone vs co-detected with other respiratory viruses. METHODS We used data from a multicenter, prospective, viral surveillance study of children seen in the emergency department and inpatient pediatric settings at seven US sites. Children less than 18 years old with fever and/or respiratory symptoms were enrolled between 12/1/16 and 10/31/18 and tested by molecular methods for HAdV, human rhinovirus/enterovirus (HRV/EV), respiratory syncytial virus (RSV), parainfluenza (PIV, types 1-4), influenza (flu, types A-C), and human metapneumovirus (HMPV). Our primary measure of illness severity was hospitalization; among hospitalized children, secondary severity outcomes included oxygen support and length of stay (LOS). RESULTS Of the 18,603 children enrolled, HAdV was detected in 1,136 (6.1%), among whom 646 (56.9%) had co-detection with at least one other respiratory virus. HRV/EV (n = 293, 45.3%) and RSV (n = 123, 19.0%) were the most frequent co-detections. Children with HRV/EV (aOR = 1.61; 95% CI = [1.11-2.34]), RSV (aOR = 4.48; 95% CI = [2.81-7.14]), HMPV (aOR = 3.39; 95% CI = [1.69-6.77]), or ≥ 2 co-detections (aOR = 1.95; 95% CI = [1.14-3.36]) had higher odds of hospitalization compared to children with HAdV alone. Among hospitalized children, HAdV co-detection with RSV or HMPV was each associated with higher odds of oxygen support, while co-detection with PIV or influenza viruses was each associated with higher mean LOS. CONCLUSIONS HAdV co-detection with other respiratory viruses was associated with greater disease severity among children with ARI compared to HAdV detection alone.
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Affiliation(s)
- Varvara Probst
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Andrew J Spieker
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Tess Stopczynski
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Laura S Stewart
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Zaid Haddadin
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City and Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Christopher J Harrison
- Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City and Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Jennifer E Schuster
- Department of Pediatrics, University of Missouri-Kansas City and Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Mary A Staat
- Department of Pediatrics, College of Medicine, University of Cincinnati and Division of Infectious Diseases, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Monica McNeal
- Department of Pediatrics, College of Medicine, University of Cincinnati and Division of Infectious Diseases, Cincinnati Children's Hospital, Cincinnati, Ohio, USA
| | - Geoffrey A Weinberg
- Department of Pediatrics, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
| | - Peter G Szilagyi
- Department of Pediatrics, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
- Department of Pediatrics, University of California at Los Angeles Mattel Children's Hospital and University of California at Los Angeles, Los Angeles, California, USA
| | - Julie A Boom
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, Texas Children's Hospital, Houston, Texas, USA
| | - Leila C Sahni
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, Texas Children's Hospital, Houston, Texas, USA
| | - Pedro A Piedra
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, Texas Children's Hospital, Houston, Texas, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas. Texas Children's Hospital, Houston, Texas, USA
| | - Janet A Englund
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, Washington, USA
| | - Eileen J Klein
- Department of Pediatrics, University of Washington School of Medicine and Seattle Children's Hospital, Seattle, Washington, USA
| | - Marian G Michaels
- Department of Pediatrics, School of Medicine, University of Pittsburgh and University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John V Williams
- Department of Pediatrics, School of Medicine, University of Pittsburgh and University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Angela P Campbell
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Manish Patel
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Susan I Gerber
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Natasha B Halasa
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
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Bentahir M, Barry MD, Koulemou K, Gala JL. Providing On-Site Laboratory and Biosafety Just-In-Time Training Inside a Box-Based Laboratory during the West Africa Ebola Outbreak: Supporting Better Preparedness for Future Health Emergencies. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph191811566. [PMID: 36141839 PMCID: PMC9517019 DOI: 10.3390/ijerph191811566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 06/13/2023]
Abstract
The Biological Light Fieldable Laboratory for Emergencies (B-LiFE) is a box-based modular laboratory with the capacity to quickly deploy on-site in cases of uncontrolled spread of infectious disease. During the 2014-2015 West Africa Ebola outbreak, this tent laboratory provided diagnostic support to the N'Zerekore Ebola Treatment Center (ETC), Guinea, for three months. One of the objectives of B-LiFE deployment was to contribute, as much as possible, to national capacity building by training local scientists. Two Guinean biologists were selected according to their basic biological knowledge and laboratory skills among 50 candidate trainees, and were integrated into the team through "just-in-time training" (JiTT), which helped the biologists acquire knowledge and laboratory skills beyond their expertise. The JiTT program was conducted according to standard laboratory procedures, in line with international biosafety guidelines adapted to field conditions. Supervised acquisition of field-laboratory practices mainly focused on biochemical testing and Ebola viral load quantification using routine PCR-based detection, including the Biofire FilmArray® system (BFA), a novel, as yet non-validated, automated assay for diagnostic testing of Ebola virus disease at the time of B-LiFE deployment. During the JiTT, the two biologists were closely involved in all laboratory activities, including BFA validation and biosafety procedures. Meanwhile, this successful JiTT enhanced the B-LiFE in-field operational capacity and contributed to national capacity building. A post-training evaluation and contacts were organised to assess the evolution and technical skills gained by the two researchers during the B-LiFE mission. At the end of the B-LiFE mission, both biologists were enrolled in follow-on programmes to curb the epidemic spreading in Africa. These results demonstrate that during infectious disease outbreaks or major crises, the JiTT approach can rapidly expand access to critical diagnostic testing and train local staff to do so.
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Affiliation(s)
- Mostafa Bentahir
- Centre for Applied Molecular Technologies (CTMA), Institute of Clinical and Experimental Research, Université Catholique de Louvain, Avenue Hippocrate 54-55, B1.54.01, B-1200 Brussels, Belgium
| | - Mamadou Diouldé Barry
- Laboratoire des Fièvres Hémorragiques Virales de Guinée, N’Zérékoré P.O. Box 50, Guinea
| | - Kekoura Koulemou
- Laboratory of the Prefectural Hospital of Gueckedou, Gueckedou P.O. Box 82, Guinea
| | - Jean-Luc Gala
- Centre for Applied Molecular Technologies (CTMA), Institute of Clinical and Experimental Research, Université Catholique de Louvain, Avenue Hippocrate 54-55, B1.54.01, B-1200 Brussels, Belgium
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Timbrook TT, Olin KE, Spaulding U, Galvin BW, Cox CB. Epidemiology of Antimicrobial Resistance Among Blood and Respiratory Specimens in the United States Using Genotypic Analysis from a Cloud-Based Population Surveillance Network. Open Forum Infect Dis 2022; 9:ofac296. [PMID: 35873295 PMCID: PMC9301484 DOI: 10.1093/ofid/ofac296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/14/2022] [Indexed: 11/26/2022] Open
Abstract
Background Antimicrobial resistance (AMR) surveillance is critical in informing strategies for infection control in slowing the spread of resistant organisms and for antimicrobial stewardship in the care of patients. However, significant challenges exist in timely and comprehensive AMR surveillance. Methods Using BioFire Pneumonia and Blood Culture 2 Panels data from BioFire Syndromic Trends (Trend), a cloud-based population surveillance network, we described the detection rate of AMR among a US cohort. Data were included from 2019 to 2021 for Gram-positive and -negative organisms and their related AMR genomic-resistant determinants as well as for detections of Candida auris. Regional and between panel AMR detection rate differences were compared. In addition, AMR codetections and detection rate per organism were evaluated for Gram-negative organisms. Results A total of 26 912 tests were performed, primarily in the Midwest. Overall, AMR detection rate was highest in the South and more common for respiratory specimens than blood. methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus detection rates were 34.9% and 15.9%, respectively, whereas AMR for Gram-negative organisms was lower with 7.0% CTX-M and 2.9% carbapenemases. In addition, 10 mcr-1 and 4 C auris detections were observed. For Gram-negative organisms, Klebsiella pneumoniae and Escherichia coli were most likely to be detected with an AMR gene, and of Gram-negative organisms, K pneumoniae was most often associated with 2 or more AMR genes. Conclusions Our study provides important in-depth evaluation of the epidemiology of AMR among respiratory and blood specimens for Gram-positive and -negative organism in the United States. The Trend surveillance network allows for near real-time surveillance of AMR.
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Affiliation(s)
- Tristan T Timbrook
- bioMérieux, Salt Lake City , Utah , United States
- University of Utah College of Pharmacy , Salt Lake City, Utah , United States
| | | | | | - Ben W Galvin
- bioMérieux, Salt Lake City , Utah , United States
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Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Marrero Rolon R, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann AC, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND, Rhoads DD. Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1. J Clin Microbiol 2022; 60:e0060022. [PMID: 35582905 PMCID: PMC9199403 DOI: 10.1128/jcm.00600-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/06/2022] [Indexed: 12/21/2022] Open
Abstract
Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene. We demonstrate that pOGTF is 98.6% sensitive and 99.9% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may affect transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly, increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.
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Affiliation(s)
- Kyle G. Rodino
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David R. Peaper
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, USA
| | - Brendan J. Kelly
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frederic Bushman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrew Marques
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hriju Adhikari
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Zheng Jin Tu
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Rebecca Marrero Rolon
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Daniel A. Green
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Gregory J. Berry
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Fann Wu
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Medini K. Annavajhala
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, New York, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, New York, USA
| | - Bijal A. Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tracy McMillen
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - N. Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Anne M. Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Robert T. Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Yale SARS-CoV-2 Genomic Surveillance Initiative
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Laboratory Medicine, Yale University, New Haven, Connecticut, USA
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
- Division of Infectious Diseases, Columbia University Irving Medical Center, New York, New York, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Infectious Disease Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Department of Pathology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Daniel D. Rhoads
- Department of Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pathology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
- Infection Biology Program, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
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A Hierarchical Genotyping Framework Using DNA Melting Temperatures Applied to Adenovirus Species Typing. Int J Mol Sci 2022; 23:ijms23105441. [PMID: 35628251 PMCID: PMC9141461 DOI: 10.3390/ijms23105441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 02/05/2023] Open
Abstract
Known genetic variation, in conjunction with post-PCR melting curve analysis, can be leveraged to provide increased taxonomic detail for pathogen identification in commercial molecular diagnostic tests. Increased taxonomic detail may be used by clinicians and public health decision-makers to observe circulation patterns, monitor for outbreaks, and inform testing practices. We propose a method for expanding the taxonomic resolution of PCR diagnostic systems by incorporating a priori knowledge of assay design and sequence information into a genotyping classification model. For multiplexed PCR systems, this framework is generalized to incorporate information from multiple assays to increase classification accuracy. An illustrative hierarchical classification model for human adenovirus (HAdV) species was developed and demonstrated ~95% cross-validated accuracy on a labeled dataset. The model was then applied to a near-real-time surveillance dataset in which deidentified adenovirus detected patient test data from 2018 through 2021 were classified into one of six adenovirus species. These results show a marked change in both the predicted prevalence for HAdV and the species makeup with the onset of the COVID-19 pandemic. HAdV-B decreased from a pre-pandemic predicted prevalence of up to 40% to less than 5% in 2021, while HAdV-A and HAdV-F species both increased in predicted prevalence.
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11
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Palmer T, Benson LS, Porucznik C, Gren LH. Impact of COVID-19 Social Distancing Mandates on Gastrointestinal Pathogen Positivity: Secondary Data Analysis. JMIR Public Health Surveill 2022; 8:e34757. [PMID: 35507923 PMCID: PMC9407155 DOI: 10.2196/34757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/10/2022] [Accepted: 05/03/2022] [Indexed: 12/01/2022] Open
Abstract
Background Acute gastrointestinal (GI) illnesses are of the most common problems evaluated by physicians and some of the most preventable. There is evidence of GI pathogen transmission when people are in close contact. The COVID-19 pandemic led to the sudden implementation of widespread social distancing measures in the United States. There is strong evidence that social distancing measures impact the spread of SARS-CoV-2, and a growing body of research indicates that these measures also decrease the transmission of other respiratory pathogens. Objective This study aims to investigate the impact of COVID-19 social distancing mandates on the GI pathogen positivity rates. Methods Deidentified GI Panel polymerase chain reaction test results from a routinely collected diagnostic database from January 1, 2019, through August 31, 2020, were analyzed for the GI pathogen positivity percentage. An interrupted time series analysis was performed, using social distancing mandate issue dates as the intervention date. The following 3 target organisms were chosen for the final analysis to represent different primary transmission routes: adenovirus F40 and 41, norovirus GI and GII, and Escherichia coli O157. Results In total, 84,223 test results from 9 states were included in the final data set. With the exception of E coli O157 in Kansas, Michigan, and Nebraska, we observed an immediate decrease in positivity percentage during the week of social distancing mandates for all other targets and states. Norovirus GI and GII showed the most notable drop in positivity, whereas E coli O157 appeared to be least impacted by social distancing mandates. Although we acknowledge the analysis has a multiple testing problem, the majority of our significant results showed significance even below the .01 level. Conclusions This study aimed to investigate the impact of social distancing mandates for COVID-19 on GI pathogen positivity, and we discovered that social distancing measures in fact decreased GI pathogen positivity initially. The use of similar measures may prove useful in GI pathogen outbreaks. The use of a unique diagnostic database in this study exhibits the potential for its use as a public health surveillance tool.
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Affiliation(s)
- Tanner Palmer
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine, 375 Chipeta WaySuite A, Salt Lake City, US.,bioMérieux, Inc, 515 Colorow Drive, Salt Lake City, US
| | - L Scott Benson
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine, 375 Chipeta WaySuite A, Salt Lake City, US
| | - Christina Porucznik
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine, 375 Chipeta WaySuite A, Salt Lake City, US
| | - Lisa H Gren
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine, 375 Chipeta WaySuite A, Salt Lake City, US
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12
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Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Rolon RM, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann AC, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND, Rhoads DD. Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.04.25.22274187. [PMID: 35547854 PMCID: PMC9094110 DOI: 10.1101/2022.04.25.22274187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mutations in the viral genome of SARS-CoV-2 can impact the performance of molecular diagnostic assays. In some cases, such as S gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here we describe partial ORF1ab gene target failure (pOGTF) on the cobas ® SARS-CoV-2 assays, defined by a ≥2 thermocycles delay in detection of the ORF1ab gene compared to the E gene. We demonstrate that pOGTF is 97% sensitive and 99% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may impact transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.
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13
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Wang C, Liu J, Mi Y, Chen J, Bi J, Chen Y. Clinical features and epidemiological analysis of respiratory human adenovirus infection in hospitalized children: a cross-sectional study in Zhejiang. Virol J 2021; 18:234. [PMID: 34844615 PMCID: PMC8628464 DOI: 10.1186/s12985-021-01705-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022] Open
Abstract
Background HAdV is one of the common pathogens in hospitalized children with acute respiratory infections (ARIs). We aim to describe the clinical and laboratory features, epidemiological characteristics, and HAdV species and/or types of inpatients with HAdV respiratory infections. Methods Respiratory samples were gathered from inpatients diagnosed ARIs in Children’s Hospital, Zhejiang University School of Medicine, and were detected by using Direct Immunofluorescence Assay from 2018 to 2019. PCR amplification and sequencing of the hypervariable zone of hexon gene were used for genotyping. The clinical and laboratory features, and HAdV genotyping, and epidemiological characteristic analysis were retrospectively performed. Results Of 7072 samples collected, 488 were identified as HAdV-positive. The overall detection rate was 6.9%. The peaked detection rate was 14.1% in January 2019. HAdV-positive cases with ARIs mainly appeared in winter. The detection rate was highest among children between 6 months and 2 years (8.7%, 123/1408). Clinical diagnosis included pneumonia (70.3%, 343/488), bronchitis (7.0%, 34/488) and acute upper respiratory tract infection (22.7%, 111/488). The common clinical manifestations were fever (93.4%, 456/488), cough (94.7%, 462/488), wheezing (26.2%, 128/488), and shortness of breath (14.8%, 72/488). 213 (43.6%) cases had co-infection and 138 (28.3%) cases had extrapulmonary symptoms. 96(19.7%) cases had intrapulmonary and intrathoracic complications.78 (16.0%) had an underlying condition, most of which were congenital heart diseases (20.5%, 16/78). The proportions of hyperpyrexia, duration of fever > 10 days, severe pneumonia, and wheezing in the co-infection group were remarkably higher than those in HAdV single-infection group (all p < 0.05). The proportions of duration of hospitalization, duration of fever > 10 days, wheezing, shortness of breath, change in level of consciousness, serosal fluids, extrapulmonary symptoms, co-infections and underlying diseases were significantly higher in severe pneumonia group than those in the mild pneumonia group (all p < 0.05). Four HAdV species were successfully identified in 155 cases and presented by 8 genotypes. HAdV-B3 (56.1%, 87/155) and HAdV -B7 (31.0%, 48/155) were the most predominant detected types and occurred commonly in different severity groups (p = 0.000), while, HAdV-B55 was detected only in the severe group. HAdV-B7’s detection rate in the severe pneumonia group was significantly higher than the non-severe pneumonia group. Conclusion HAdV detection rate is related to age and season. Bronchopneumonia accounts for about 70% HAdV-positive inpatients. The common clinical manifestations include hyperpyrexia, cough, wheezing, and shortness of breath. HAdV-B3 and HAdV-B7 are the most common types in children diagnosed with respiration infections.
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Affiliation(s)
- Caiyun Wang
- Department of Infectious Disease, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, 3333 Binsheng Road, Hangzhou, 310052, China.
| | - Juanjuan Liu
- Department of Infectious Disease, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, 3333 Binsheng Road, Hangzhou, 310052, China
| | - Yumei Mi
- Department of Infectious Disease, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, 3333 Binsheng Road, Hangzhou, 310052, China
| | - Jing Chen
- Department of Infectious Disease, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, 3333 Binsheng Road, Hangzhou, 310052, China
| | - Jing Bi
- Department of Otolaryngology-Head and Neck Surgery, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, 3333 Binsheng Road, Hangzhou, 310052, China
| | - Yinghu Chen
- Department of Infectious Disease, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, National Children's Regional Medical Center, 3333 Binsheng Road, Hangzhou, 310052, China
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14
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Rothman RE, Hsieh YH, DuVal A, Talan DA, Moran GJ, Krishnadasan A, Shaw-Saliba K, Dugas AF. Front-Line Emergency Department Clinician Acceptability and Use of a Prototype Real-Time Cloud-Based Influenza Surveillance System. Front Public Health 2021; 9:740258. [PMID: 34805066 PMCID: PMC8601200 DOI: 10.3389/fpubh.2021.740258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Objectives: To assess emergency department (ED) clinicians' perceptions of a novel real-time influenza surveillance system using a pre- and post-implementation structured survey. Methods: We created and implemented a laboratory-based real-time influenza surveillance system at two EDs at the beginning of the 2013-2014 influenza season. Patients with acute respiratory illness were tested for influenza using rapid PCR-based Cepheid Xpert Flu assay. Results were instantaneously uploaded to a cloud-based data aggregation system made available to clinicians via a web-based dashboard. Clinicians received bimonthly email updates summating year-to-date results. Clinicians were surveyed prior to, and after the influenza season, to assess their views regarding acceptability and utility of the surveillance system data which were shared via dashboard and email updates. Results: The pre-implementation survey revealed that the majority (82%) of the 151 ED clinicians responded that they “sporadically” or “don't,” actively seek influenza-related information during the season. However, most (75%) reported that they would find additional information regarding influenza prevalence useful. Following implementation, there was an overall increase in the frequency of clinician self-reporting increased access to surveillance information from 50 to 63%, with the majority (75%) indicating that the surveillance emails impacted their general awareness of influenza. Clinicians reported that the additional real-time surveillance data impacted their testing (65%) and treatment (51%) practices. Conclusions: The majority of ED clinicians found surveillance data useful and indicated the additional information impacted their clinical practice. Accurate and timely surveillance information, distributed in a provider-friendly format could impact ED clinician management of patients with suspected influenza.
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Affiliation(s)
- Richard E Rothman
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Yu-Hsiang Hsieh
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Anna DuVal
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - David A Talan
- Ronald Reagan University of California, Los Angeles (UCLA) Medical Center, Los Angeles, CA, United States
| | - Gregory J Moran
- University of California, Olive-View Medical Center, Los Angeles, CA, United States
| | - Anusha Krishnadasan
- University of California, Olive-View Medical Center, Los Angeles, CA, United States
| | - Katy Shaw-Saliba
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Andrea F Dugas
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD, United States
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15
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Benedetti G, Krause TG, Schneider UV, Lisby JG, Voldstedlund M, Bang D, Trebbien R, Emborg HD. Spotlight influenza: Influenza surveillance before and after the introduction of point-of-care testing in Denmark, season 2014/15 to 2018/19. Euro Surveill 2021; 26. [PMID: 34533117 PMCID: PMC8447826 DOI: 10.2807/1560-7917.es.2021.26.37.2000724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background In Denmark, influenza surveillance is ensured by data capturing from existing population-based registers. Since 2017, point-of-care (POC) testing has been implemented outside the regional clinical microbiology departments (CMD). Aim We aimed to assess influenza laboratory results in view of the introduction of POC testing. Methods We retrospectively observed routine surveillance data on national influenza tests before and after the introduction of POC testing as available in the Danish Microbiological Database. Also, we conducted a questionnaire study among Danish CMD about influenza diagnostics. Results Between the seasons 2014/15 and 2018/19, 199,744 influenza tests were performed in Denmark of which 44,161 were positive (22%). After the introduction of POC testing, the overall percentage of positive influenza tests per season did not decrease. The seasonal influenza test incidence was higher in all observed age groups. The number of operating testing platforms placed outside a CMD and with an instrument analytical time ≤ 3 h increased after 2017. Regionally, the number of tests registered as POC in the Danish Microbiological Database and the number of tests performed with an instrument analytical time ≤ 3 h or outside a CMD partially differed. Where comparable (71% of tests), the relative proportion of POC tests out of all tests increased from season 2017/18 to 2018/19. In both seasons, the percentage of positive POC tests resulted slightly lower than for non-POC tests. Conclusion POC testing integrated seamlessly into national influenza surveillance. We propose the use of POC results in the routine surveillance of seasonal influenza.
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Affiliation(s)
- Guido Benedetti
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Tyra Grove Krause
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Uffe Vest Schneider
- Department of Clinical Microbiology, Copenhagen University Hospital, Amager and Hvidovre, Copenhagen, Denmark
- Department of Clinical Microbiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Jan Gorm Lisby
- Department of Clinical Microbiology, Copenhagen University Hospital, Amager and Hvidovre, Copenhagen, Denmark
| | - Marianne Voldstedlund
- Department of Data Integration and Analysis, Statens Serum Institut, Copenhagen, Denmark
| | - Didi Bang
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Microbiology, Copenhagen University Hospital, Amager and Hvidovre, Copenhagen, Denmark
| | - Ramona Trebbien
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Hanne-Dorthe Emborg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
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16
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Turtle J, Riley P, Ben-Nun M, Riley S. Accurate influenza forecasts using type-specific incidence data for small geographic units. PLoS Comput Biol 2021; 17:e1009230. [PMID: 34324487 PMCID: PMC8354478 DOI: 10.1371/journal.pcbi.1009230] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 08/10/2021] [Accepted: 06/30/2021] [Indexed: 11/24/2022] Open
Abstract
Influenza incidence forecasting is used to facilitate better health system planning and could potentially be used to allow at-risk individuals to modify their behavior during a severe seasonal influenza epidemic or a novel respiratory pandemic. For example, the US Centers for Disease Control and Prevention (CDC) runs an annual competition to forecast influenza-like illness (ILI) at the regional and national levels in the US, based on a standard discretized incidence scale. Here, we use a suite of forecasting models to analyze type-specific incidence at the smaller spatial scale of clusters of nearby counties. We used data from point-of-care (POC) diagnostic machines over three seasons, in 10 clusters, capturing: 57 counties; 1,061,891 total specimens; and 173,909 specimens positive for Influenza A. Total specimens were closely correlated with comparable CDC ILI data. Mechanistic models were substantially more accurate when forecasting influenza A positive POC data than total specimen POC data, especially at longer lead times. Also, models that fit subpopulations of the cluster (individual counties) separately were better able to forecast clusters than were models that directly fit to aggregated cluster data. Public health authorities may wish to consider developing forecasting pipelines for type-specific POC data in addition to ILI data. Simple mechanistic models will likely improve forecast accuracy when applied at small spatial scales to pathogen-specific data before being scaled to larger geographical units and broader syndromic data. Highly local forecasts may enable new public health messaging to encourage at-risk individuals to temporarily reduce their social mixing during seasonal peaks and guide public health intervention policy during potentially severe novel influenza pandemics.
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Affiliation(s)
- James Turtle
- Infectious Disease Group, Predictive Science Inc., San Diego, California, United States
- * E-mail:
| | - Pete Riley
- Infectious Disease Group, Predictive Science Inc., San Diego, California, United States
| | - Michal Ben-Nun
- Infectious Disease Group, Predictive Science Inc., San Diego, California, United States
| | - Steven Riley
- Infectious Disease Group, Predictive Science Inc., San Diego, California, United States
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom
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17
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Ruzante JM, Olin K, Munoz B, Nawrocki J, Selvarangan R, Meyers L. Real-time gastrointestinal infection surveillance through a cloud-based network of clinical laboratories. PLoS One 2021; 16:e0250767. [PMID: 33930062 PMCID: PMC8087049 DOI: 10.1371/journal.pone.0250767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 04/14/2021] [Indexed: 02/04/2023] Open
Abstract
Acute gastrointestinal infection (AGI) represents a significant public health concern. To control and treat AGI, it is critical to quickly and accurately identify its causes. The use of novel multiplex molecular assays for pathogen detection and identification provides a unique opportunity to improve pathogen detection, and better understand risk factors and burden associated with AGI in the community. In this study, de-identified results from BioFire® FilmArray® Gastrointestinal (GI) Panel were obtained from January 01, 2016 to October 31, 2018 through BioFire® Syndromic Trends (Trend), a cloud database. Data was analyzed to describe the occurrence of pathogens causing AGI across United States sites and the relative rankings of pathogens monitored by FoodNet, a CDC surveillance system were compared. During the period of the study, the number of tests performed increased 10-fold and overall, 42.6% were positive for one or more pathogens. Seventy percent of the detections were bacteria, 25% viruses, and 4% parasites. Clostridium difficile, enteropathogenic Escherichia coli (EPEC) and norovirus were the most frequently detected pathogens. Seasonality was observed for several pathogens including astrovirus, rotavirus, and norovirus, EPEC, and Campylobacter. The co-detection rate was 10.2%. Enterotoxigenic E. coli (ETEC), Plesiomonas shigelloides, enteroaggregative E. coli (EAEC), and Entamoeba histolytica were detected with another pathogen over 60% of the time, while less than 30% of C. difficile and Cyclospora cayetanensis were detected with another pathogen. Positive correlations among co-detections were found between Shigella/Enteroinvasive E. coli with E. histolytica, and ETEC with EAEC. Overall, the relative ranking of detections for the eight GI pathogens monitored by FoodNet and BioFire Trend were similar for five of them. AGI data from BioFire Trend is available in near real-time and represents a rich data source for the study of disease burden and GI pathogen circulation in the community, especially for those pathogens not often targeted by surveillance.
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Affiliation(s)
- Juliana M Ruzante
- Center for Environmental Health, Risk and Sustainability, RTI International, Research Triangle Park, North Carolina, United States of America
| | - Katherine Olin
- Biomathematics, BioFire Diagnostics, Salt Lake City, Utah, United States of America
| | - Breda Munoz
- Center for Environmental Health, Risk and Sustainability, RTI International, Research Triangle Park, North Carolina, United States of America
| | - Jeff Nawrocki
- Biomathematics, BioFire Diagnostics, Salt Lake City, Utah, United States of America
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, Missouri, United States of America
| | - Lindsay Meyers
- Medical Data Systems, BioFire Diagnostics, Salt Lake City, Utah, United States of America
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18
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Park SW, Pons-Salort M, Messacar K, Cook C, Meyers L, Farrar J, Grenfell BT. Epidemiological dynamics of enterovirus D68 in the United States and implications for acute flaccid myelitis. Sci Transl Med 2021; 13:13/584/eabd2400. [PMID: 33692131 DOI: 10.1126/scitranslmed.abd2400] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/24/2020] [Accepted: 02/08/2021] [Indexed: 01/02/2023]
Abstract
Acute flaccid myelitis (AFM) recently emerged in the United States as a rare but serious neurological condition since 2012. Enterovirus D68 (EV-D68) is thought to be a main causative agent, but limited surveillance of EV-D68 in the United States has hampered the ability to assess their causal relationship. Using surveillance data from the BioFire Syndromic Trends epidemiology network in the United States from January 2014 to September 2019, we characterized the epidemiological dynamics of EV-D68 and found latitudinal gradient in the mean timing of EV-D68 cases, which are likely climate driven. We also demonstrated a strong spatiotemporal association of EV-D68 with AFM. Mathematical modeling suggested that the recent dominant biennial cycles of EV-D68 dynamics may not be stable. Nonetheless, we predicted that a major EV-D68 outbreak, and hence an AFM outbreak, would have still been possible in 2020 under normal epidemiological conditions. Nonpharmaceutical intervention efforts due to the ongoing COVID-19 pandemic are likely to have reduced the sizes of EV-D68 and AFM outbreaks in 2020, illustrating the broader epidemiological impact of the pandemic.
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Affiliation(s)
- Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA.
| | - Margarita Pons-Salort
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - Kevin Messacar
- Department of Pediatrics, Sections of Hospital Medicine and Infectious Diseases, University of Colorado, Aurora, CO 80045, USA.,Children's Hospital Colorado, Aurora, CO 80045, USA
| | - Camille Cook
- BioFire Diagnostics LLC, 515 Colorow Drive, Salt Lake City, UT 84108, USA
| | - Lindsay Meyers
- BioFire Diagnostics LLC, 515 Colorow Drive, Salt Lake City, UT 84108, USA
| | - Jeremy Farrar
- Wellcome Trust, Gibbs Building, 215 Euston Road, London NW1 2BE, UK
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA.,Princeton School of Public and International Affairs, Princeton University, Princeton, NJ 08540, USA.,Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
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19
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Nawrocki J, Olin K, Holdrege MC, Hartsell J, Meyers L, Cox C, Powell M, Cook CV, Jones J, Robbins T, Hemmert A, Ginocchio CC. The Effects of Social Distancing Policies on Non-SARS-CoV-2 Respiratory Pathogens. Open Forum Infect Dis 2021; 8:ofab133. [PMID: 34322558 PMCID: PMC7989184 DOI: 10.1093/ofid/ofab133] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/15/2021] [Indexed: 11/12/2022] Open
Abstract
Background The initial focus of the US public health response to coronavirus disease 2019 (COVID-19) was the implementation of numerous social distancing policies. While COVID-19 was the impetus for imposing these policies, it is not the only respiratory disease affected by their implementation. This study aimed to assess the impact of social distancing policies on non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) respiratory pathogens typically circulating across multiple US states. Methods Linear mixed-effect models were implemented to explore the effects of 5 social distancing policies on non-SARS-CoV-2 respiratory pathogens across 9 states from January 1 through May 1, 2020. The observed 2020 pathogen detection rates were compared week by week with historical rates to determine when the detection rates were different. Results Model results indicate that several social distancing policies were associated with a reduction in total detection rate, by nearly 15%. Policies were associated with decreases in pathogen circulation of human rhinovirus/enterovirus and human metapneumovirus, as well as influenza A, which typically decrease after winter. Parainfluenza viruses failed to circulate at historical levels during the spring. The total detection rate in April 2020 was 35% less than the historical average. Many of the pathogens driving this difference fell below the historical detection rate ranges within 2 weeks of initial policy implementation. Conclusions This analysis investigated the effect of multiple social distancing policies implemented to reduce transmission of SARS-CoV-2 on non-SARS-CoV-2 respiratory pathogens. These findings suggest that social distancing policies may be used as an impactful public health tool to reduce communicable respiratory illness.
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Affiliation(s)
| | | | | | | | | | - Charles Cox
- BioFire Diagnostics, LLC, Salt Lake City, Utah, USA
| | | | | | - Jay Jones
- BioFire Diagnostics, LLC, Salt Lake City, Utah, USA
| | - Tom Robbins
- BioFire Diagnostics, LLC, Salt Lake City, Utah, USA
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20
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Park SW, Farrar J, Messacar K, Meyers L, Pons-Salort M, Grenfell BT. Epidemiological dynamics of enterovirus D68 in the US: implications for acute flaccid myelitis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.07.23.20069468. [PMID: 32766605 PMCID: PMC7402064 DOI: 10.1101/2020.07.23.20069468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The lack of active surveillance for enterovirus D68 (EV-D68) in the US has hampered the ability to assess the relationship with predominantly biennial epidemics of acute flaccid myelitis (AFM), a rare but serious neurological condition. Using novel surveillance data from the BioFire® Syndromic Trends (Trend) epidemiology network, we characterize the epidemiological dynamics of EV-D68 and demonstrate strong spatiotemporal association with AFM. Although the recent dominant biennial cycles of EV-D68 dynamics may not be stable, we show that a major EV-D68 epidemic, and hence an AFM outbreak, would still be possible in 2020 under normal epidemiological conditions. Significant social distancing due to the ongoing COVID-19 pandemic could reduce the size of an EV-D68 epidemic in 2020, illustrating the potential broader epidemiological impact of the pandemic.
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Affiliation(s)
- Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
| | - Jeremy Farrar
- Wellcome Trust, Gibbs Building, 215 Euston Road, London NW1 2BE, UK
| | - Kevin Messacar
- Department of Pediatrics, Sections of Hospital Medicine and Infectious Diseases, University of Colorado, Aurora, CO 80045, USA
- Children’s Hospital Colorado, Aurora, CO, USA
| | - Lindsay Meyers
- BioFire Diagnostics, LLC 515 Colorow Drive, Salt Lake City, UT 84108 USA
| | - Margarita Pons-Salort
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, Norfolk Place, London W2 1PG, UK
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
- Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ 08540, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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21
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Probst V, Datyner EK, Haddadin Z, Rankin DA, Hamdan L, Rahman HK, Spieker A, Stewart LS, Guevara C, Yepsen E, Schmitz JE, Halasa NB. Human adenovirus species in children with acute respiratory illnesses. J Clin Virol 2021; 134:104716. [PMID: 33360858 PMCID: PMC8324062 DOI: 10.1016/j.jcv.2020.104716] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/21/2020] [Accepted: 12/06/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Human adenovirus (HAdV) species B, C, and E are commonly associated with acute respiratory illnesses (ARI). We sought to determine the association between HAdV species and ARI severity in children over one respiratory season at Monroe Carell Jr. Children's Hospital at Vanderbilt. METHODS We conducted a retrospective cohort study of children with HAdV from a provider-ordered BioFire® FilmArray Respiratory Pathogen Panel 2.0 (RPP) from 05/2018-06/2019. Type-specific PCR assays for HAdV-B3, B7, B11, B14, B16, B21, HAdV-C1, C2, C5, C6, and HAdV-E4 were performed. Demographics, clinical characteristics, and outcome data were compared between HAdV species. RESULTS Of 4514 respiratory specimens collected, 2644 (59 %) had at least one pathogen detected by RPP, and 384 (15 %) were HAdV-positive; 342 (89 %) were available for research testing with 306 (89 %) specimens from unique symptomatic individuals; 237 (77 %) were positive for the following species: 104 (44 %) HAdV-B, 114 (48 %) HAdV-C, 9 (4%) HAdV-E, and 10 (4%) with co-detection between species. The majority with identified HAdV species were seen in the ED (62 %), and approximately one-third were hospitalized. Patients with HAdV-C were more likely to be younger, hospitalized, and have a higher frequency of seizures compared to HAdV-B. CONCLUSION HAdV-C and HAdV-B were the most common species detected, with differences in clinical characteristics and outcomes noted. Additional studies with larger sample sizes focusing on a high-risk pediatric population are necessary to determine if differences in illness severity across individual HAdV types exist to guide further type-specific HAdV vaccine development.
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Affiliation(s)
- Varvara Probst
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA.
| | - Emily K Datyner
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Zaid Haddadin
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Danielle A Rankin
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA; Vanderbilt Epidemiology PhD Program, Vanderbilt University School of Medicine, 1161 21st Ave S, Nashville, TN, 37232, USA
| | - Lubna Hamdan
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Herdi K Rahman
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Andrew Spieker
- Department of Biostatistics, Vanderbilt University Medical Center, 2525 West End Ave #1100, Nashville, TN, 37203, USA
| | - Laura S Stewart
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Claudia Guevara
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Erin Yepsen
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
| | - Jonathan E Schmitz
- Departments of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1211 Medical Center Dr, Nashville, TN, 37232, USA
| | - Natasha B Halasa
- Departments of Pediatrics, Vanderbilt University Medical Center, 1161 21st Ave. South, Nashville, TN, 37232, USA
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22
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Couturier MR, Bard JD. Direct-from-Specimen Pathogen Identification: Evolution of Syndromic Panels. Clin Lab Med 2020; 39:433-451. [PMID: 31383267 PMCID: PMC7131637 DOI: 10.1016/j.cll.2019.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Marc Roger Couturier
- ARUP Laboratories, University of Utah, 500 Chipeta Way, Salt Lake City, UT 84108, USA.
| | - Jennifer Dien Bard
- Microbiology and Virology Laboratories, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, University of Southern California, 4650 Sunset Boulevard MS#32, Los Angeles, CA 90027, USA
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23
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Scarpino SV, Scott JG, Eggo RM, Clements B, Dimitrov NB, Meyers LA. Socioeconomic bias in influenza surveillance. PLoS Comput Biol 2020; 16:e1007941. [PMID: 32644990 PMCID: PMC7347107 DOI: 10.1371/journal.pcbi.1007941] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/11/2020] [Indexed: 11/18/2022] Open
Abstract
Individuals in low socioeconomic brackets are considered at-risk for developing influenza-related complications and often exhibit higher than average influenza-related hospitalization rates. This disparity has been attributed to various factors, including restricted access to preventative and therapeutic health care, limited sick leave, and household structure. Adequate influenza surveillance in these at-risk populations is a critical precursor to accurate risk assessments and effective intervention. However, the United States of America's primary national influenza surveillance system (ILINet) monitors outpatient healthcare providers, which may be largely inaccessible to lower socioeconomic populations. Recent initiatives to incorporate Internet-source and hospital electronic medical records data into surveillance systems seek to improve the timeliness, coverage, and accuracy of outbreak detection and situational awareness. Here, we use a flexible statistical framework for integrating multiple surveillance data sources to evaluate the adequacy of traditional (ILINet) and next generation (BioSense 2.0 and Google Flu Trends) data for situational awareness of influenza across poverty levels. We find that ZIP Codes in the highest poverty quartile are a critical vulnerability for ILINet that the integration of next generation data fails to ameliorate.
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Affiliation(s)
- Samuel V. Scarpino
- Network Science Institute, Northeastern University, Boston, Massachusetts, United States of America
- Marine & Environmental Sciences, Northeastern University, Boston, Massachusetts, United States of America
- Physics, Northeastern University, Boston, Massachusetts, United States of America
- Health Sciences, Northeastern University, Boston, Massachusetts, United States of America
- ISI Foundation, Turin, Italy
| | - James G. Scott
- Department of Statistics and Data Sciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Rosalind M. Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Bruce Clements
- Pediatric Healthcare Connection, Austin, Texas, United States of America
| | - Nedialko B. Dimitrov
- Department of Operations Research, The University of Texas at Austin, Austin, Texas, United States of America
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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24
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Inagaki A, Kitano T, Nishikawa H, Suzuki R, Onaka M, Nishiyama A, Kitagawa D, Oka M, Masuo K, Yoshida S. The Epidemiology of Admission-Requiring Pediatric Respiratory Infections in a Japanese Community Hospital Using Multiplex PCR. Jpn J Infect Dis 2020; 74:23-28. [PMID: 32611977 DOI: 10.7883/yoken.jjid.2020.154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Respiratory tract infections (RTIs) are the most common diseases globally among children. This study aimed to assess the epidemiology of admission-requiring pediatric RTI cases and evaluate the effect of the pathogen type on the length of hospital stay (LOS) using the FilmArray® respiratory panel, a multiplex PCR test. The age-specific distribution and seasonality of viruses were investigated between March 26, 2018 and April 12, 2019. Multivariable linear regression analyses were performed to evaluate the effect of pathogen type and coinfection on LOS. Among 153 hospitalized RTI patients, respiratory syncytial virus was the leading cause of hospitalization in infants < 12 months of age (27.7%). Human metapneumovirus and parainfluenza virus were also major causes of hospitalization in patients aged 2-3 years (22.6% and 22.6%, respectively). In the multivariable linear regression model excluding rhinovirus/enterovirus, there was a significant association between viral coinfection and longer LOS (p = 0.012), while single viral infection of any type was not positively correlated with LOS. This study revealed the epidemiology of admission-requiring pediatric RTIs.
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Affiliation(s)
- Atsushi Inagaki
- Department of Pediatrics, Nara Prefecture General Medical Center, Japan
| | - Taito Kitano
- Division of Infectious Diseases, The Hospital for Sick Children, Canada
| | - Hiroki Nishikawa
- Department of Pediatrics, Nara Prefecture General Medical Center, Japan
| | - Rika Suzuki
- Department of Pediatrics, Nara Prefecture General Medical Center, Japan
| | - Masayuki Onaka
- Department of Pediatrics, Nara Prefecture General Medical Center, Japan
| | - Atsuko Nishiyama
- Department of Pediatrics, Nara Prefecture General Medical Center, Japan
| | - Daisuke Kitagawa
- Department of Microbiology, Nara Prefecture General Medical Center, Japan
| | - Miyako Oka
- Department of Microbiology, Nara Prefecture General Medical Center, Japan
| | - Kazue Masuo
- Department of Microbiology, Nara Prefecture General Medical Center, Japan
| | - Sayaka Yoshida
- Department of Pediatrics, Nara Prefecture General Medical Center, Japan
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25
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Lieberman NAP, Peddu V, Xie H, Shrestha L, Huang ML, Mears MC, Cajimat MN, Bente DA, Shi PY, Bovier F, Roychoudhury P, Jerome KR, Moscona A, Porotto M, Greninger AL. In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.22.165225. [PMID: 32607510 PMCID: PMC7325176 DOI: 10.1101/2020.06.22.165225] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Despite limited genomic diversity, SARS-CoV-2 has shown a wide range of clinical manifestations in different patient populations. The mechanisms behind these host differences are still unclear. Here, we examined host response gene expression across infection status, viral load, age, and sex among shotgun RNA-sequencing profiles of nasopharyngeal swabs from 430 individuals with PCR-confirmed SARS-CoV-2 and 54 negative controls. SARS-CoV-2 induced a strong antiviral response with upregulation of antiviral factors such as OAS1-3 and IFIT1-3 , and Th1 chemokines CXCL9/10/11 , as well as a reduction in transcription of ribosomal proteins. SARS-CoV-2 culture in human airway epithelial cultures replicated the in vivo antiviral host response. Patient-matched longitudinal specimens (mean elapsed time = 6.3 days) demonstrated reduction in interferon-induced transcription, recovery of transcription of ribosomal proteins, and initiation of wound healing and humoral immune responses. Expression of interferon-responsive genes, including ACE2 , increased as a function of viral load, while transcripts for B cell-specific proteins and neutrophil chemokines were elevated in patients with lower viral load. Older individuals had reduced expression of Th1 chemokines CXCL9/10/11 and their cognate receptor, CXCR3 , as well as CD8A and granzyme B, suggesting deficiencies in trafficking and/or function of cytotoxic T cells and natural killer (NK) cells. Relative to females, males had reduced B and NK cell-specific transcripts and an increase in inhibitors of NF-κB signaling, possibly inappropriately throttling antiviral responses. Collectively, our data demonstrate that host responses to SARS-CoV-2 are dependent on viral load and infection time course, with observed differences due to age and sex that may contribute to disease severity.
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26
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Mommert M, Tabone O, Guichard A, Oriol G, Cerrato E, Denizot M, Cheynet V, Pachot A, Lepape A, Monneret G, Venet F, Brengel-Pesce K, Textoris J, Mallet F. Dynamic LTR retrotransposon transcriptome landscape in septic shock patients. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2020; 24:96. [PMID: 32188504 PMCID: PMC7081582 DOI: 10.1186/s13054-020-2788-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/14/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated host response to infection. Numerous studies have explored the complex and dynamic transcriptome modulations observed in sepsis patients, but a large fraction of the transcriptome remains unexplored. This fraction could provide information to better understand sepsis pathophysiology. Multiple levels of interaction between human endogenous retroviruses (HERV) and the immune response have led us to hypothesize that sepsis is associated with HERV transcription and that HERVs may contribute to a signature among septic patients allowing stratification and personalized management. METHODS We used a high-density microarray and RT-qPCR to evaluate the HERV and Mammalian Apparent Long Terminal Repeat retrotransposons (MaLR) transcriptome in a pilot study that included 20 selected septic shock patients, stratified on mHLA-DR expression, with samples collected on day 1 and day 3 after inclusion. We validated the results in an unselected, independent cohort that included 100 septic shock patients on day 3 after inclusion. We compared septic shock patients, according to their immune status, to describe the transcriptional HERV/MaLR and conventional gene expression. For differential expression analyses, moderated t tests were performed and Wilcoxon signed-rank tests were used to analyze RT-qPCR results. RESULTS We showed that 6.9% of the HERV/MaLR repertoire was transcribed in the whole blood, and septic shock was associated with an early modulation of a few thousand of these loci, in comparison to healthy volunteers. We provided evidence that a subset of HERV/MaLR and conventional genes were differentially expressed in septic shock patients, according to their immune status, using monocyte HLA-DR (mHLA-DR) expression as a proxy. A group of 193 differentially expressed HERV/MaLR probesets, tested in an independent septic shock cohort, identified two groups of patients with different immune status and severity features. CONCLUSION We demonstrated that a large, unexplored part of our genome, which codes for HERV/MaLR, may be linked to the host immune response. The identified set of HERV/MaLR probesets should be evaluated on a large scale to assess the relevance of these loci in the stratification of septic shock patients. This may help to address the heterogeneity of these patients.
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Affiliation(s)
- Marine Mommert
- Joint Research Unit, bioMerieux, Centre Hospitalier Lyon Sud, Hospice Civils de Lyon, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France. .,EA 7426 Pathophysiology of Injury-Induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôspital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France.
| | - Olivier Tabone
- EA 7426 Pathophysiology of Injury-Induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôspital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France
| | - Audrey Guichard
- Joint Research Unit, bioMerieux, Centre Hospitalier Lyon Sud, Hospice Civils de Lyon, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France.,EA 7426 Pathophysiology of Injury-Induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôspital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France
| | - Guy Oriol
- Joint Research Unit, bioMerieux, Centre Hospitalier Lyon Sud, Hospice Civils de Lyon, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Elisabeth Cerrato
- EA 7426 Pathophysiology of Injury-Induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôspital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France
| | - Mélanie Denizot
- EA 7426 Pathophysiology of Injury-Induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôspital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France
| | - Valérie Cheynet
- Joint Research Unit, bioMerieux, Centre Hospitalier Lyon Sud, Hospice Civils de Lyon, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Alexandre Pachot
- EA 7426 Pathophysiology of Injury-Induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôspital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France
| | - Alain Lepape
- Intensive Care Unit, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France.,Emerging Pathogens Laboratory, Epidemiology and International Health, International Center for Infectiology Research (CIRI), Lyon, France.,bioMérieux Joint Research Unit, Hospices Civils de Lyon, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Guillaume Monneret
- EA 7426 Pathophysiology of Injury-Induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôspital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France.,Immunology Laboratory, Hospices Civils de Lyon, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Fabienne Venet
- EA 7426 Pathophysiology of Injury-Induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôspital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France.,Immunology Laboratory, Hospices Civils de Lyon, Groupement Hospitalier Edouard Herriot, Lyon, France
| | - Karen Brengel-Pesce
- Joint Research Unit, bioMerieux, Centre Hospitalier Lyon Sud, Hospice Civils de Lyon, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France
| | - Julien Textoris
- EA 7426 Pathophysiology of Injury-Induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôspital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France.,Department of Anaesthesiology and Critical Care Medicine, Hospices Civils de Lyon, Groupement Hospitalier Edouard Herriot, Université Claude Bernard Lyon 1, Lyon, France
| | - François Mallet
- Joint Research Unit, bioMerieux, Centre Hospitalier Lyon Sud, Hospice Civils de Lyon, 165 Chemin du Grand Revoyet, 69310, Pierre-Benite, France.,EA 7426 Pathophysiology of Injury-Induced Immunosuppression, University of Lyon1-Hospices Civils de Lyon-bioMérieux, Hôspital Edouard Herriot, 5 Place d'Arsonval, 69437, Lyon Cedex 3, France
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27
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Meyers L, Dien Bard J, Galvin B, Nawrocki J, Niesters HGM, Stellrecht KA, St George K, Daly JA, Blaschke AJ, Robinson C, Wang H, Cook CV, Hassan F, Dominguez SR, Pretty K, Naccache S, Olin KE, Althouse BM, Jones JD, Ginocchio CC, Poritz MA, Leber A, Selvarangan R. Enterovirus D68 outbreak detection through a syndromic disease epidemiology network. J Clin Virol 2020; 124:104262. [PMID: 32007841 DOI: 10.1016/j.jcv.2020.104262] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 02/04/2023]
Abstract
BACKGROUND In 2014, enterovirus D68 (EV-D68) was responsible for an outbreak of severe respiratory illness in children, with 1,153 EV-D68 cases reported across 49 states. Despite this, there is no commercial assay for its detection in routine clinical care. BioFire® Syndromic Trends (Trend) is an epidemiological network that collects, in near real-time, deidentified. BioFire test results worldwide, including data from the BioFire® Respiratory Panel (RP). OBJECTIVES Using the RP version 1.7 (which was not explicitly designed to differentiate EV-D68 from other picornaviruses), we formulate a model, Pathogen Extended Resolution (PER), to distinguish EV-D68 from other human rhinoviruses/enteroviruses (RV/EV) tested for in the panel. Using PER in conjunction with Trend, we survey for historical evidence of EVD68 positivity and demonstrate a method for prospective real-time outbreak monitoring within the network. STUDY DESIGN PER incorporates real-time polymerase chain reaction metrics from the RPRV/EV assays. Six institutions in the United States and Europe contributed to the model creation, providing data from 1,619 samples spanning two years, confirmed by EV-D68 gold-standard molecular methods. We estimate outbreak periods by applying PER to over 600,000 historical Trend RP tests since 2014. Additionally, we used PER as a prospective monitoring tool during the 2018 outbreak. RESULTS The final PER algorithm demonstrated an overall sensitivity and specificity of 87.1% and 86.1%, respectively, among the gold-standard dataset. During the 2018 outbreak monitoring period, PER alerted the research network of EV-D68 emergence in July. One of the first sites to experience a significant increase, Nationwide Children's Hospital, confirmed the outbreak and implemented EV-D68 testing at the institution in response. Applying PER to the historical Trend dataset to determine rates among RP tests, we find three potential outbreaks with predicted regional EV-D68 rates as high as 37% in 2014, 16% in 2016, and 29% in 2018. CONCLUSIONS Using PER within the Trend network was shown to both accurately predict outbreaks of EV-D68 and to provide timely notifications of its circulation to participating clinical laboratories.
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Affiliation(s)
- Lindsay Meyers
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Jennifer Dien Bard
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA 90027, United States; Keck School of Medicine, University of Southern California, Los Angeles, CA 90039, United States.
| | - Ben Galvin
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Jeff Nawrocki
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Hubert G M Niesters
- The University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Division of Clinical Virology, Groningen, The Netherlands.
| | - Kathleen A Stellrecht
- Department of Pathology and Laboratory Medicine, Albany Medical Center, Albany, NY 12208, United States.
| | - Kirsten St George
- New York State Department of Health, Albany, NY, 12202, United States.
| | - Judy A Daly
- Department of Pathology, University of Utah, Salt Lake City, UT 84132, United States; Division of Inpatient Medicine, Primary Children's Hospital, Salt Lake City, UT 84132, United States.
| | - Anne J Blaschke
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84132, United States.
| | - Christine Robinson
- Department of Pathology and Laboratory Medicine, Children's Colorado, Aurora, CO 80045, United States.
| | - Huanyu Wang
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH 43205, United States.
| | - Camille V Cook
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Ferdaus Hassan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, United States.
| | - Sam R Dominguez
- Department of Pathology and Laboratory Medicine, Children's Colorado, Aurora, CO 80045, United States.
| | - Kristin Pretty
- Department of Pathology and Laboratory Medicine, Children's Colorado, Aurora, CO 80045, United States.
| | - Samia Naccache
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA 90027, United States.
| | | | - Benjamin M Althouse
- Information School, University of Washington, Seattle, WA, 98105, United States; Department of Biology, New Mexico State University, Las Cruces, NM, 88003, United States.
| | - Jay D Jones
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States.
| | - Christine C Ginocchio
- BioFire Diagnostics, Salt Lake City, UT, 84103, United States; Global Medical Affairs, bioMérieux, Durham, NC 27712, United States; Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, United States.
| | - Mark A Poritz
- BioFire Defense, Salt Lake City, UT 84107, United States.
| | - Amy Leber
- Department of Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH 43205, United States.
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Hospital, Kansas City, MO 64108, United States.
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28
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Sobczyk J, Jain S, Sun X, Karris M, Wooten D, Stagnaro J, Reed S. Comparison of Multiplex Gastrointestinal Pathogen Panel and Conventional Stool Testing for Evaluation of Patients With HIV Infection. Open Forum Infect Dis 2020; 7:ofz547. [PMID: 31976355 PMCID: PMC6970129 DOI: 10.1093/ofid/ofz547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/02/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Gastrointestinal pathogen panels (GPPs) are increasingly used to identify stool pathogens, but their impact in people with HIV (PWH) is unknown. We performed a retrospective cohort study comparing GPP and conventional stool evaluation in PWH. METHODS We included all PWH who underwent GPP (Biofire Diagnostics; implemented September 15, 2015) or conventional testing, including stool culture, Clostridium difficile polymerase chain reaction testing, fluorescent smears for Cryptosporidium or Giardia, and ova and parasite exams (O&P) from 2013 to 2017. A total of 1941 specimens were tested, with 169 positive specimens detected in 144 patients. We compared result turnaround time, pathogen co-infection, antibiotic treatment, and treatment outcomes between positive specimens detected by conventional testing vs GPP. RESULTS Overall, 124 patient samples tested positive by GPP, compared with 45 patient specimens by conventional testing. The GPP group demonstrated a higher co-infection rate (48.4% vs 13.3%; P < .001) and quicker turnaround time (23.4 vs 71.4 hours; P < .001). The GPP identified 29 potential viral infections that were undetectable by conventional stool tests. Unnecessary anti-infective therapy was avoided in 9 of 11 exclusively viral infections. Exclusively nonpathogenic parasites (n = 13) were detected by conventional stool tests, the majority of which were treated with metronidazole. There were no significant differences in clinical outcomes between groups. CONCLUSIONS In PWH, GPP implementation improved antibiotic stewardship through shorter turnaround times and detection of enteric viral pathogens.
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Affiliation(s)
- Juliana Sobczyk
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Sonia Jain
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, California, USA
| | - Xiaoying Sun
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, California, USA
| | - Maile Karris
- Department of Internal Medicine, University of California, San Diego, La Jolla, California, USA
| | - Darcy Wooten
- Department of Internal Medicine, University of California, San Diego, La Jolla, California, USA
| | - Janet Stagnaro
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Sharon Reed
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
- Department of Internal Medicine, University of California, San Diego, La Jolla, California, USA
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29
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Degeling C, Gilbert GL, Tambyah P, Johnson J, Lysaght T. One Health and Zoonotic Uncertainty in Singapore and Australia: Examining Different Regimes of Precaution in Outbreak Decision-Making. Public Health Ethics 2019. [DOI: 10.1093/phe/phz017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
A One Health approach holds great promise for attenuating the risk and burdens of emerging infectious diseases (EIDs) in both human and animal populations. Because the course and costs of EID outbreaks are difficult to predict, One Health policies must deal with scientific uncertainty, whilst addressing the political, economic and ethical dimensions of communication and intervention strategies. Drawing on the outcomes of parallel Delphi surveys conducted with policymakers in Singapore and Australia, we explore the normative dimensions of two different precautionary approaches to EID decision-making—which we call regimes of risk management and organizing uncertainty, respectively. The imperative to act cautiously can be seen as either an epistemic rule or as a decision rule, which has implications for how EID uncertainty is managed. The normative features of each regime, and their implications for One Health approaches to infectious disease risks and outbreaks, are described. As One Health attempts to move upstream to prevent rather than react to emergence of EIDs in humans, we show how the approaches to uncertainty, taken by experts and decision-makers, and their choices about the content and quality of evidence, have implications for who pays the price of precaution, and, thereby, social and global justice.
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Affiliation(s)
- C Degeling
- Australian Centre for Health Engagement, Evidence and Values, School of Health and Society, University of Wollongong and Sydney Health Ethics, School of Public Health, University of Sydney
| | - G L Gilbert
- Sydney Health Ethics, School of Public Health, University of Sydney and Marie Bashir Institute of Infectious Diseases and Biosecurity
| | - P Tambyah
- Department of Medicine, National University of Singapore and National University Health System
| | - J Johnson
- Sydney Health Ethics, School of Public Health, University of Sydney and Marie Bashir Institute of Infectious Diseases and Biosecurity
| | - T Lysaght
- Centre for Biomedical Ethics, National University of Singapore
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30
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de Lusignan S, Hoang U, Liyanage H, Yonova I, Ferreira F, Diez-Domingo J, Clark T. Feasibility of Point-of-Care Testing for Influenza Within a National Primary Care Sentinel Surveillance Network in England: Protocol for a Mixed Methods Study. JMIR Res Protoc 2019; 8:e14186. [PMID: 31710303 PMCID: PMC6878097 DOI: 10.2196/14186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/16/2019] [Accepted: 08/14/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Point-of-care testing (POCT) for influenza promises to provide real-time information to influence clinical decision making and improve patient outcomes. Public Health England has published a toolkit to assist implementation of these tests in the UK National Health Service. OBJECTIVE A feasibility study will be undertaken to assess the implementation of influenza POCT in primary care as part of a sentinel surveillance network. METHODS We will conduct a mixed methods study to compare the sampling rates in practices using POCT and current virology swabbing practices not using POCT, and to understand the issues and barriers to implementation of influenza POCT in primary care workflows. The study will take place between March and May 2019. It will be nested in general practices that are part of the English national sentinel surveillance network run by the Royal College of General Practitioners Research and Surveillance Centre. The primary outcome is the number of valid influenza swabs taken and tested by the practices involved in the study using the new POCT. RESULTS A total of 6 practices were recruited, and data collection commenced on March 11, 2019. Moreover, 312 swab samples had been collected at the time of submission of the protocol, which was 32.5% (312/960) of the expected sample size. In addition, 68 samples were positive for influenza, which was 20.1% (68/338) of the expected sample size. CONCLUSIONS To the best of our knowledge, this is the first time an evaluation study has been undertaken on POCT for influenza in general practice in the United Kingdom. This proposed study promises to shed light on the feasibility of implementation of POCT in primary care and on the views of practitioners about the use of influenza POCT in primary care, including its impact on primary care workflows. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/14186.
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Affiliation(s)
- Simon de Lusignan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, United Kingdom
- Department of Clinical and Experimental Medicine, University of Surrey, Guildford, United Kingdom
| | - Uy Hoang
- Department of Clinical and Experimental Medicine, University of Surrey, Guildford, United Kingdom
| | - Harshana Liyanage
- Department of Clinical and Experimental Medicine, University of Surrey, Guildford, United Kingdom
| | - Ivelina Yonova
- Department of Clinical and Experimental Medicine, University of Surrey, Guildford, United Kingdom
| | - Filipa Ferreira
- Department of Clinical and Experimental Medicine, University of Surrey, Guildford, United Kingdom
| | - Javier Diez-Domingo
- Vaccine Research Department, Foundation for the Promotion of Health and Biomedical Research in the Valencian Region, Valencia, Spain
| | - Tristan Clark
- Academic Unit of Clinical and Experimental Sciences, University of Southampton, Southampton, United Kingdom
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31
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George DB, Taylor W, Shaman J, Rivers C, Paul B, O'Toole T, Johansson MA, Hirschman L, Biggerstaff M, Asher J, Reich NG. Technology to advance infectious disease forecasting for outbreak management. Nat Commun 2019; 10:3932. [PMID: 31477707 PMCID: PMC6718692 DOI: 10.1038/s41467-019-11901-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/07/2019] [Indexed: 12/17/2022] Open
Abstract
Forecasting is beginning to be integrated into decision-making processes for infectious disease outbreak response. We discuss how technologies could accelerate the adoption of forecasting among public health practitioners, improve epidemic management, save lives, and reduce the economic impact of outbreaks.
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Affiliation(s)
| | | | - Jeffrey Shaman
- Climate and Health Program, Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Caitlin Rivers
- Center for Health Security, Johns Hopkins University, Baltimore, MD, USA
| | | | | | - Michael A Johansson
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, PR, USA
| | | | - Matthew Biggerstaff
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Nicholas G Reich
- Department of Biostatistics and Epidemiology, University of Massachusetts-Amherst, Amherst, MA, USA
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32
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[Utility of multiplex PCR (FilmArray Blood Culture Identification) in other biological liquids. Detection of Streptococcus pyogenes in brain abscess and synovial fluid]. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2019; 32:194-197. [PMID: 30841692 PMCID: PMC6441981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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33
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López-Amor L, Escudero D, Fernández J, Martín-Iglesias L, Viña L, Fernández-Suárez J, Leal-Negredo Á, Leoz B, Álvarez-García L, Castelló-Abietar C, Boga JA, Vázquez F. [Meningitis/Encephalitis diagnosis in ICU using Multiplex PCR system: Is it time of change?]. REVISTA ESPANOLA DE QUIMIOTERAPIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE QUIMIOTERAPIA 2019; 32:246-253. [PMID: 30980520 PMCID: PMC6609945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE To evaluate the clinical impact of Meningitis/Encephalitis FilmArray® panel for the diagnosis of cerebral nervous system infection and to compare the results (including time for diagnosis) with those obtained by conventional microbiological techniques. METHODS A prospective observational study in an Intensive Care Unit of adults from a tertiary hospital was carried out. Cerebrospinal fluid from all patients was taken by lumbar puncture and assessed by the meningitis/encephalitis FilmArray® panel ME, cytochemical study, Gram, and conventional microbiological cultures. RESULTS A total of 21 patients admitted with suspicion of Meningitis/Encephalitis. Median age of patients was 58.4 years (RIQ 38.1-67.3), median APACHE II 18 (RIQ 12-24). Median stay in ICU and median hospital stay was 4 (RIQ 2-6) and 17 days (RIQ 14-28), respectively. The overall mortality was 14.3%. A final clinical diagnosis of meningitis or encephalitis was established in 16 patients, obtaining the etiological diagnosis in 12 of them (75%). The most frequent etiology was Streptococcus pneumoniae (8 cases). FilmArray® allowed etiological diagnosis in 3 cases in which the culture had been negative, and the results led to changes in the empirical antimicrobial therapy in 7 of 16 cases (43.8%). FilmArray® yielded a global sensitivity and specificity of 100% and 90%, respectively. The median time to obtain results from the latter and conventional culture (including antibiogram) was 2.9 hours (RIQ 2.1-3.8) and 45.1 hours (RIQ 38.9-58.7), respectively. CONCLUSIONS The Meningitis/Encephalitis FilmArray® panel was able to establish the etiologic diagnosis faster than conventional methods. Also, it achieved a better sensitivity and led to prompt targeted antimicrobial therapy.
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Affiliation(s)
- Lucía López-Amor
- Servicio de Medicina Intensiva. Hospital Universitario Central de Asturias, Oviedo. España,Grupo de Investigación Microbiología Traslacional del ISPA (Instituto de Investigación Sanitaria del Principado de Asturias),Correspondencia: Lucía López-Amor Servicio de Medicina Intensiva. Hospital Universitario Central de Asturias. Avenida de Roma s/n 33011 Oviedo. Teléfono 985108000 Extensión 38162.Fax 985108777 E-mail:
| | - Dolores Escudero
- Servicio de Medicina Intensiva. Hospital Universitario Central de Asturias, Oviedo. España,Grupo de Investigación Microbiología Traslacional del ISPA (Instituto de Investigación Sanitaria del Principado de Asturias)
| | - Javier Fernández
- Grupo de Investigación Microbiología Traslacional del ISPA (Instituto de Investigación Sanitaria del Principado de Asturias),Servicio de Microbiología. Hospital Universitario Central de Asturias, Oviedo. España
| | - Lorena Martín-Iglesias
- Servicio de Medicina Intensiva. Hospital Universitario Central de Asturias, Oviedo. España,Grupo de Investigación Microbiología Traslacional del ISPA (Instituto de Investigación Sanitaria del Principado de Asturias)
| | - Lucía Viña
- Servicio de Medicina Intensiva. Hospital Universitario Central de Asturias, Oviedo. España,Grupo de Investigación Microbiología Traslacional del ISPA (Instituto de Investigación Sanitaria del Principado de Asturias)
| | - Jonathan Fernández-Suárez
- Grupo de Investigación Microbiología Traslacional del ISPA (Instituto de Investigación Sanitaria del Principado de Asturias),Servicio de Microbiología. Hospital Universitario Central de Asturias, Oviedo. España
| | - Álvaro Leal-Negredo
- Grupo de Investigación Microbiología Traslacional del ISPA (Instituto de Investigación Sanitaria del Principado de Asturias),Servicio de Microbiología. Hospital Universitario Central de Asturias, Oviedo. España
| | - Blanca Leoz
- Servicio de Medicina Intensiva. Hospital Universitario Central de Asturias, Oviedo. España,Grupo de Investigación Microbiología Traslacional del ISPA (Instituto de Investigación Sanitaria del Principado de Asturias)
| | - Laura Álvarez-García
- Servicio de Medicina Intensiva. Hospital Universitario Central de Asturias, Oviedo. España,Grupo de Investigación Microbiología Traslacional del ISPA (Instituto de Investigación Sanitaria del Principado de Asturias)
| | - Cristian Castelló-Abietar
- Grupo de Investigación Microbiología Traslacional del ISPA (Instituto de Investigación Sanitaria del Principado de Asturias),Servicio de Microbiología. Hospital Universitario Central de Asturias, Oviedo. España
| | - José Antonio Boga
- Grupo de Investigación Microbiología Traslacional del ISPA (Instituto de Investigación Sanitaria del Principado de Asturias),Servicio de Microbiología. Hospital Universitario Central de Asturias, Oviedo. España
| | - Fernando Vázquez
- Grupo de Investigación Microbiología Traslacional del ISPA (Instituto de Investigación Sanitaria del Principado de Asturias),Servicio de Microbiología. Hospital Universitario Central de Asturias, Oviedo. España,Departamento de Biología Funcional, Universidad de Oviedo, Oviedo. España.,Fundación de Investigación Oftalmológica, Instituto Oftalmológico Fernández-Vega, Oviedo. España
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Tang YW, Stratton CW. Multiplex PCR for Detection and Identification of Microbial Pathogens. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2018. [PMCID: PMC7121544 DOI: 10.1007/978-3-319-95111-9_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Multiplexed nucleic acid-based tests for infectious disease have become a standard part of clinical laboratory practice. These tests provide a comprehensive syndrome-based approach to determine the etiological agent of disease. The technology underlying these different systems is reviewed here with a special focus on the BioFire FilmArray® platform. The literature on the clinical utility and cost-effectiveness of these platforms for respiratory, blood culture, and gastrointestinal infections is discussed. Although there are reports showing a clear benefit to the patient or to the healthcare system from adopting a syndromic molecular approach, it is also apparent that clinical laboratories and healthcare providers are still learning how to take full advantage of the new systems. Finally, some improvements to this technology that should appear in the next few years are discussed. These include automated pathogen-specific surveillance based on aggregating the data from these systems, a move toward point-of-care syndromic testing, and further decreases in time to result of the tests.
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Affiliation(s)
- Yi-Wei Tang
- Departments of Laboratory Medicine and Internal Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology and Immunology and Medicine, Vanderbilt University Medical Center, Nashville, TN USA
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