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Varga Z, Bueno-Marí R, Risueño Iranzo J, Kurucz K, Tóth GE, Zana B, Zeghbib S, Görföl T, Jakab F, Kemenesi G. Accelerating targeted mosquito control efforts through mobile West Nile virus detection. Parasit Vectors 2024; 17:140. [PMID: 38500161 PMCID: PMC10949795 DOI: 10.1186/s13071-024-06231-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/03/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Different mosquito control strategies have been implemented to mitigate or prevent mosquito-related public health situations. Modern mosquito control largely relies on multiple approaches, including targeted, specific treatments. Given this, it is becoming increasingly important to supplement these activities with rapid and mobile diagnostic capacities for mosquito-borne diseases. We aimed to create and test the applicability of a rapid diagnostic system for West Nile virus that can be used under field conditions. METHODS In this pilot study, various types of adult mosquito traps were applied within the regular mosquito monitoring activity framework for mosquito control. Then, the captured specimens were used for the detection of West Nile virus RNA under field conditions with a portable qRT-PCR approach within 3-4 h. Then, positive samples were subjected to confirmatory RT-PCR or NGS sequencing in the laboratory to obtain genome information of the virus. We implemented phylogenetic analysis to characterize circulating strains. RESULTS A total of 356 mosquito individuals representing 7 species were processed in 54 pools, each containing up to 20 individuals. These pools were tested for the presence of West Nile virus, and two pools tested positive, containing specimens from the Culex pipiens and Anopheles atroparvus mosquito species. As a result of subsequent sequencing, we present the complete genome of West Nile virus and Bagaza virus. CONCLUSIONS The rapid identification of infected mosquitoes is the most important component of quick response adulticide or larvicide treatments to prevent human cases. The conceptual framework of real-time surveillance can be optimized for other pathogens and situations not only in relation to West Nile virus. We present an early warning system for mosquito-borne diseases and demonstrate its application to aid rapid-response mosquito control actions.
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Affiliation(s)
- Zsaklin Varga
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Rubén Bueno-Marí
- Department of Research and Development, Laboratorios Lokímica, Valencia, Spain
- Parasite & Health Research Group, Department of Pharmacy, Pharmaceutical Technology and Parasitology, Faculty of Pharmacy, University of Valencia, Valencia, Spain
| | - José Risueño Iranzo
- Department of Research and Development, Laboratorios Lokímica, Valencia, Spain
| | - Kornélia Kurucz
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Gábor Endre Tóth
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Brigitta Zana
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Safia Zeghbib
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Tamás Görföl
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Gábor Kemenesi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary.
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Thomas JK, Clark J, Arora V, Burgess DS, Burgess DR, Mynatt RP, VanHoose JD, Wallace KL, Cotner SE. Performance of ePlex® blood culture identification panels in clinical isolates and characterization of antimicrobial stewardship opportunities. Diagn Microbiol Infect Dis 2024; 109:116269. [PMID: 38692201 DOI: 10.1016/j.diagmicrobio.2024.116269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 05/03/2024]
Abstract
We assessed the performance of GenMark's ePlex® Blood Culture Identification (BCID) Panels for overall agreement of organism identification and resistance mechanism detection with standard microbiologic methods. This study included patients with a positive blood culture from May 2020 to January 2021. The primary outcomes were to assess concordance of ePlex® organism identification with standard identification methods and concordance of ePlex® genotypic resistance mechanism detection with standard phenotypic susceptibility testing. Secondary outcomes included panel specific performance and characterization of antimicrobial stewardship opportunities. The overall identification concordance rate in 1276 positive blood cultures was 98.1%. The overall concordance for the presence of resistance markers was 98.2% and concordance for the absence of resistance markers was 100%. A majority of ePlex® results (69.5%) represented opportunities for potential antimicrobial stewardship intervention. High concordance rates between the ePlex® BCID panels and standard identification and susceptibility methods enable utilization of results to guide rapid antimicrobial optimization.
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Affiliation(s)
- Jenni K Thomas
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Justin Clark
- University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Vaneet Arora
- University of Kentucky College of Medicine, Lexington, KY, USA; Department of Pathology and Laboratory Medicine, University of Kentucky HealthCare, Lexington, KY, USA
| | - David S Burgess
- University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Donna R Burgess
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Ryan P Mynatt
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Jeremy D VanHoose
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA
| | - Katie L Wallace
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA
| | - Sarah E Cotner
- Department of Pharmacy Services, University of Kentucky HealthCare, Lexington, KY, USA; University of Kentucky College of Pharmacy, Lexington, KY, USA.
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Simms LA, Davies C, Jayasundara N, Sandhu S, Pintara A, Pretorius A, Nimmo GR, Harper J, Hiskens M, Smith K, Boxall S, Lord A, Giardino R, Farlow D, Ward DM, Huygens F. Performance evaluation of InfectID-BSI: A rapid quantitative PCR assay for detecting sepsis-associated organisms directly from whole blood. J Microbiol Methods 2023:106783. [PMID: 37442279 DOI: 10.1016/j.mimet.2023.106783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/15/2023]
Abstract
BACKGROUND Bloodstream infections (BSIs) (presence of pathogenic organism in blood) that progress to sepsis (life-threatening organ dysfunction caused by the body's dysregulated response to an infection) is a major healthcare issue globally with close to 50 million cases annually and 11 million sepsis-related deaths, representing about 20% of all global deaths. A rapid diagnostic assay with accurate pathogen identification has the potential to improve antibiotic stewardship and clinical outcomes. METHODS The InfectID-Bloodstream Infection (InfectID-BSI) test is a real-time quantitative PCR assay, which detects 26 of the most prevalent BSI-causing pathogens (bacteria and yeast) directly from blood (without need for pre-culture). InfectID-BSI identifies pathogens using highly discriminatory single nucleotide polymorphisms located in conserved regions of bacterial and fungal genomes. This report details the findings of a patient study which compared InfectID-BSI with conventional blood culture at two public hospitals in Queensland, Australia, using 375 whole blood samples (from multiple anatomical sites, eg. left arm, right arm, etc.) from 203 patients that have been clinically assessed to have signs and symptoms of suspected BSI, sepsis and septic shock. FINDINGS InfectID-BSI was a more sensitive method for microorganism detection compared with blood culture (BacT/ALERT, bioMerieux) for positivity rate (102 vs 54 detections), detection of fastidious organisms (Streptococcus pneumoniae and Aerococcus viridans) (25 vs 0), detection of low bioburden infections (measured as genome copies/0.35 mL of blood), time to result (<3 h including DNA extraction for InfectID-BSI vs 16 h-48 h for blood culture), and volume of blood required for testing (0.5 mL vs 40-60 mL). InfectID-BSI is an excellent 'rule out' test for BSI, with a negative predictive value of 99.7%. InfectID-BSI's ability to detect 'difficult to culture' microorganisms re-defines the four most prevalent BSI-associated pathogens as E. coli (28.4%), S. pneumoniae (17.6%), S. aureus (13.7%), and S. epidermidis (13.7%). INTERPRETATION InfectID-BSI has the potential to alter the clinical treatment pathway for patients with BSIs that are at risk of progressing to sepsis.
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Affiliation(s)
- Lisa A Simms
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia.
| | - Corey Davies
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Nadeesha Jayasundara
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Sumeet Sandhu
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia; Queensland Health, Brisbane, Queensland, Australia
| | - Alexander Pintara
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Amorette Pretorius
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Graeme R Nimmo
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia; School of Medicine, Griffith University, Gold Coast, Queensland, Australia
| | - Jacqueline Harper
- Pathology Queensland, Royal Brisbane and Women's Hospital, Brisbane, Queensland 4029, Australia
| | - Matthew Hiskens
- Mackay Institute of Research and Innovation, Mackay Hospital and Health Service, Mackay, Queensland 4740, Australia
| | - Karen Smith
- Mackay Institute of Research and Innovation, Mackay Hospital and Health Service, Mackay, Queensland 4740, Australia; Department of Emergency Medicine, Mackay Hospital and Health Service, Mackay, Queensland 4740, Australia
| | - Sarah Boxall
- Department of Emergency Medicine, Mackay Hospital and Health Service, Mackay, Queensland 4740, Australia
| | - Anton Lord
- Spectroscopy and Data Consultants, Brisbane, Queensland, Australia
| | - Raffaella Giardino
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - David Farlow
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia; Mackay Institute of Research and Innovation, Mackay Hospital and Health Service, Mackay, Queensland 4740, Australia
| | | | - Flavia Huygens
- Microbio Ltd., Translational Research Institute, Brisbane, Queensland 4102, Australia
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Jeffrey M, Denny KJ, Lipman J, Conway Morris A. Differentiating infection, colonisation, and sterile inflammation in critical illness: the emerging role of host-response profiling. Intensive Care Med 2023; 49:760-771. [PMID: 37344680 DOI: 10.1007/s00134-023-07108-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023]
Abstract
Infection results when a pathogen produces host tissue damage and elicits an immune response. Critically ill patients experience immune activation secondary to both sterile and infectious insults, with overlapping clinical phenotypes and underlying immunological mechanisms. Patients also undergo a shift in microbiota with the emergence of pathogen-dominant microbiomes. Whilst the combination of inflammation and microbial shift has long challenged intensivists in the identification of true infection, the advent of highly sensitive molecular diagnostics has further confounded the diagnostic dilemma as the number of microbial detections increases. Given the key role of the host immune response in the development and definition of infection, profiling the host response offers the potential to help unravel the conundrum of distinguishing colonisation and sterile inflammation from true infection. This narrative review provides an overview of current approaches to distinguishing colonisation from infection using routinely available techniques and proposes matrices to support decision-making in this setting. In searching for new tools to better discriminate these states, the review turns to the understanding of the underlying pathobiology of the host response to infection. It then reviews the techniques available to assess this response in a clinically applicable context. It will cover techniques including profiling of transcriptome, protein expression, and immune functional assays, detailing the current state of knowledge in diagnostics along with the challenges and opportunities. The ultimate infection diagnostic tool will likely combine an assessment of both host immune response and sensitive pathogen detection to improve patient management and facilitate antimicrobial stewardship.
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Affiliation(s)
- Mark Jeffrey
- John V Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Division of Anaesthesia, Department of Medicine, Level 4, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK
| | - Kerina J Denny
- Department of Intensive Care, Gold Coast University Hospital, Southport, QLD, Australia
- School of Medicine, University of Queensland, Herston, Brisbane, Australia
| | - Jeffrey Lipman
- University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Australia
- Jamieson Trauma Institute and Intensive Care Services, Royal Brisbane and Women's Hospital, Brisbane, Australia
- Nimes University Hospital, University of Montpellier, Nimes, France
| | - Andrew Conway Morris
- John V Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Division of Anaesthesia, Department of Medicine, Level 4, Addenbrooke's Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK.
- Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK.
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Jang YO, Kim NH, Roh Y, Koo B, Lee HJ, Kim JY, Kim SH, Shin Y. Self-directed molecular diagnostics (SdMDx) system for COVID-19 via one-pot processing. Sens Actuators B Chem 2023; 378:133193. [PMID: 36570722 PMCID: PMC9759472 DOI: 10.1016/j.snb.2022.133193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/03/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Rapid, sensitive, and specific detection of the severe acute respiratory syndrome coronavirus (SARS-CoV)- 2 during early infection is pivotal in controlling the spread and pathological progression of Coronavirus Disease 2019 (COVID-19). Thus, highly accurate, affordable, and scalable point-of-care (POC) diagnostic technologies are necessary. Herein, we developed a rapid and efficient self-directed molecular diagnostic (SdMDx) system for SARS-CoV-2. This system combines the sample preparation step, including virus enrichment and extraction processes, which involve dimethyl suberimidate dihydrochloride and diatomaceous earth functionalized with 3-aminopropyl(diethoxy)methylsilane, and the detection step using loop-mediated isothermal amplification-lateral flow assay (LAMP-LFA). Using the SdMDx system, SARS-CoV-2 could be detected within 47 min by hand without the need for any larger instruments. The SdMDx system enabled detection as low as 0.05 PFU in the culture fluid of SARS-CoV-2-infected VeroE6 cells. We validated the accuracy of the SdMDx system on 38 clinical nasopharyngeal specimens. The clinical utility of the SdMDx system for targeting the S gene of SARS-CoV-2 showed 94.4% sensitivity and 100% specificity. This system is more sensitive than antigen and antibody assays, and it minimizes the use of complicated processes and reduces contamination risks. Accordingly, we demonstrated that the SdMDx system enables a rapid, accurate, simple, efficient, and inexpensive detection of SARS-CoV-2 at home, in emergency facilities, and in low-resource sites as a pre-screening platform and POC testing through self-operation and self-diagnosis.
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Affiliation(s)
- Yoon Ok Jang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Nam Hun Kim
- INFUSIONTECH, 38 Heungan-daero, 427 beon-gil, Dongan-gu, Anyang-si 14059, Republic of Korea
| | - Yeonjeong Roh
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Bonhan Koo
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Hyo Joo Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Songpa-gu, Seoul 05505, Republic of Korea
| | - Yong Shin
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
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Donnars A, Mahieu R, Declerck C, Chenouard R, Lemarié C, Pailhoriès H, Requin J, Kempf M, Eveillard M. BIOFIRE® Blood Culture IDentification 2 (BCID2) panel for early adaptation of antimicrobial therapy in adult patients with bloodstream infections: a real-life experience. Diagn Microbiol Infect Dis 2023; 105:115858. [PMID: 36442386 DOI: 10.1016/j.diagmicrobio.2022.115858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/24/2022] [Accepted: 11/05/2022] [Indexed: 11/13/2022]
Abstract
Our objective was to assess the effectiveness of a multiplex PCR panel for blood culture identification (BCID2) on the implementation of appropriate antimicrobial therapy. We conducted a monocentric pre/post study comparing the time to result from direct microscopic examination (DE) to bacterial identification (BI) in positive blood cultures between 2 different periods: P1 without BCID2 and P2 with BCID2. Appropriate treatments prescribed before DE and after DE / BCID2 and after BI / BCID2 were compared using direct proportion comparison and survival analysis. For mono-microbial bloodstream infections, the proportion of appropriate antimicrobial treatment after DE was 50% in P1 vs. 87.5% after BCID2 in P2 (P < 0.001) for Gram-negative bacteria and 33.0% in P1 vs. 64.4% in P2 (P < 0.01) for Gram-positive bacteria. A significant difference (P = 0.04) was recorded with survival curves for Gram positive bacteria. BCID2 seems effective in reducing the time for prescribing appropriate antimicrobials.
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Affiliation(s)
- Anne Donnars
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Rafael Mahieu
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France
| | - Charles Declerck
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France
| | - Rachel Chenouard
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Carole Lemarié
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Hélène Pailhoriès
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France
| | - Jim Requin
- Service des Maladies Infectieuses et Tropicales, CHU Angers, Angers, France
| | - Marie Kempf
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France
| | - Matthieu Eveillard
- Laboratoire de Bactériologie, Département de Biologie des Agents Infectieux, CHU Angers, Angers, France; Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, INCIT, Angers, France.
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Stokes W, Venner AA, Buss E, Tipples G, Berenger BM. Prospective population-level validation of the Abbott ID NOW severe acute respiratory syndrome coronavirus 2 device implemented in multiple settings for testing asymptomatic and symptomatic individuals. Clin Microbiol Infect 2023; 29:247-52. [PMID: 36096431 DOI: 10.1016/j.cmi.2022.08.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Diagnostic evaluation of the ID NOW coronavirus disease 2019 (COVID-19) assay in various real-world settings among symptomatic and asymptomatic individuals. METHODS Depending on the setting, the ID NOW testing was performed using oropharyngeal swabs (OPSs) taken from patients with symptoms suggestive of COVID-19, asymptomatic close contacts, or asymptomatic individuals as part of outbreak point prevalence screening. From January to April 2021, a select number of sites switched from using OPS to combined oropharyngeal and nasal swab (O + NS) for ID NOW testing. For every individual tested, two swabs were collected by a health care worker: one swab (OPS or O + NS) for ID NOW testing and a separate swab (OPS or nasopharyngeal swab) for RT-PCR. RESULTS A total of 129 112 paired samples were analysed (16 061 RT-PCR positive). Of these, 81 697 samples were from 42 COVID-19 community collection sites, 16 924 samples were from 69 rural hospitals, 1927 samples were from nine emergency shelters and addiction treatment facilities, 23 802 samples were from six mobile units that responded to 356 community outbreaks, and 4762 O + NS swabs were collected from three community collection sites and one emergency shelter. The ID NOW assay sensitivity was the highest among symptomatic individuals presenting to community collection sites (92.5%; 95% CI, 92.0-93.0%) and the lowest for asymptomatic individuals associated with community outbreaks (73.9%; 95% CI, 69.8-77.7%). Specificity was >99% in all populations tested. DISCUSSION The sensitivity of ID NOW severe acute respiratory syndrome coronavirus 2 testing is the highest when used in symptomatic community populations not seeking medical care. Sensitivity and positive predictive value drop by approximately 10% when tested on asymptomatic populations. Using combined oropharyngeal and nasal swabs did not improve the performance of ID NOW assay.
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Jakobsen N, Goecke NB, Pedersen KS. Evaluation of the diagnostic performance of a commercially available point-of-care test for post weaning diarrhoea in pigs-a pilot study. Porcine Health Manag 2022; 8:49. [PMID: 36503595 PMCID: PMC9743710 DOI: 10.1186/s40813-022-00292-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 11/01/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Post weaning diarrhoea is expected to become an increasing problem in pig herds following the outphasing of medicinal Zinc Oxide. Currently, no equally effective substitute has been found and an increase in metaphylactic batch medication with antibiotics is expected. However, prudent use of antibiotics is needed to mitigate antibiotic resistance development and one option could be pre-treatment diagnostics. Employing a point-of-care test in a herd could provide fast diagnostics and help guide antibiotic treatment. Hence, the aim of this study was to evaluate the diagnostic performance of a commercially available point-of-care test for enterotoxigenic Escherichia coli (ETEC) F4, ETEC F18 and rotavirus in weaned pigs. RESULTS In total 115 diarrheic samples from two conventional herds were included in the evaluation of the Rainbow Piglet Scours test, which was compared to microbiological PCR analyses. The comparison yielded a diagnostic sensitivity, diagnostic specificity, positive and negative predictive value of 0.28, 0.99, 0.92 and 0.70 for ETEC F4, 0.40, 0.92, 0.91 and 0.45 for ETEC F18 and 0.67, 0.88, 0.91 and 0.61 for rotavirus. CONCLUSIONS The point-of-care test yielded a low diagnostic sensitivity and a high diagnostic specificity for ETEC F4, ETEC F18 and rotavirus. Due to the high level of false negatives, the test cannot be recommended for individual diagnostics on pig-level.
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Affiliation(s)
- Nadia Jakobsen
- grid.5254.60000 0001 0674 042XDepartment of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Nicole Bakkegård Goecke
- grid.5254.60000 0001 0674 042XDepartment of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - Ken Steen Pedersen
- grid.5254.60000 0001 0674 042XDepartment of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
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Serigstad S, Ritz C, Faurholt-Jepsen D, Markussen D, Ebbesen MH, Kommedal Ø, Bjørneklett RO, Heggelund L, Clark TW, van Werkhoven CH, Knoop ST, Ulvestad E, Grewal HMS. Impact of rapid molecular testing on diagnosis, treatment and management of community-acquired pneumonia in Norway: a pragmatic randomised controlled trial (CAPNOR). Trials 2022; 23:622. [PMID: 35915452 PMCID: PMC9340738 DOI: 10.1186/s13063-022-06467-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background Community-acquired pneumonia (CAP) causes a large burden of disease. Due to difficulties in obtaining representative respiratory samples and insensitive standard microbiological methods, the microbiological aetiology of CAP is difficult to ascertain. With a few exceptions, standard-of-care diagnostics are too slow to influence initial decisions on antimicrobial therapy. The management of CAP is therefore largely based on empirical treatment guidelines. Empiric antimicrobial therapy is often initiated in the primary care setting, affecting diagnostic tests based on conventional bacterial culture in hospitalized patients. Implementing rapid molecular testing may improve both the proportion of positive tests and the time it takes to obtain test results. Both measures are important for initiation of pathogen-targeted antibiotics, involving rapid de-escalation or escalation of treatment, which may improve antimicrobial stewardship and potentially patient outcome. Methods Patients presenting to the emergency department of Haukeland University Hospital (HUH) in Bergen, Norway, will be screened for inclusion into a pragmatic randomised controlled trial (RCT). Eligible patients with a suspicion of CAP will be included and randomised to receive either standard-of-care methods (standard microbiological testing) or standard-of-care methods in addition to testing by the rapid and comprehensive real-time multiplex PCR panel, the BioFire® FilmArray® Pneumonia Panel plus (FAP plus) (bioMérieux S.A., Marcy-l’Etoile, France). The results of the FAP plus will be communicated directly to the treating staff within ~2 h of sampling. Discussion We will examine if rapid use of FAP plus panel in hospitalized patients with suspected CAP can improve both the time to and the proportion of patients receiving pathogen-directed treatment, thereby shortening the exposure to unnecessary antibiotics and the length of hospital admission, compared to the standard-of-care arm. The pragmatic design together with broad inclusion criteria and a straightforward intervention could make our results generalizable to other similar centres. Trial registration ClinicalTrials.govNCT04660084. Registered on December 9, 2020 Supplementary Information The online version contains supplementary material available at 10.1186/s13063-022-06467-7.
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Affiliation(s)
- Sondre Serigstad
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Christian Ritz
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, Faculty of Medicine, University of Bergen, Bergen, Norway. .,National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark.
| | | | - Dagfinn Markussen
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
| | - Marit H Ebbesen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Øyvind Kommedal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, Faculty of Medicine, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Rune O Bjørneklett
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Lars Heggelund
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, Faculty of Medicine, University of Bergen, Bergen, Norway.,Department of Internal Medicine, Vestre Viken Hospital Trust, Drammen, Norway
| | - Tristan W Clark
- School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Cornelis H van Werkhoven
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Siri T Knoop
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Elling Ulvestad
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, Faculty of Medicine, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Harleen M S Grewal
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship cluster, Faculty of Medicine, University of Bergen, Bergen, Norway. .,Department of Microbiology, Haukeland University Hospital, Bergen, Norway.
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10
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Zhao Y, Lin K, Zhang H, Yuan G, Zhang Y, Pan J, Hong L, Huang Y, Ye Y, Huang L, Chen X, Liu J, Li X, He X, Yue Q, Zhang H, Zhou A, Zhuang Y, Chen J, Wu C, Zhou W, Cai F, Zhang S, Li L, Li S, Bian T, Li J, Yin J, Ruan Z, Xu S, Zhang Y, Chen J, Zhang Y, Han J, Su T, Tu F, Jiang L, Lei C, Du Q, Ai J, Zhang W. Evaluation of droplet digital PCR rapid detection method and precise diagnosis and treatment for suspected sepsis (PROGRESS): a study protocol for a multi-center pragmatic randomized controlled trial. BMC Infect Dis 2022; 22:630. [PMID: 35854212 PMCID: PMC9295283 DOI: 10.1186/s12879-022-07557-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022] Open
Abstract
Background Sepsis is still a major public health concern and a medical emergency due to its high morbidity and mortality. Accurate and timely etiology diagnosis is crucial for sepsis management. As an emerging rapid and sensitive pathogen detection tool, digital droplet PCR (ddPCR) has shown promising potential in rapid identification of pathogens and antimicrobial resistance genes. However, the diagnostic value and clinical impact of ddPCR tests remains to be studied in patients with suspected sepsis. PROGRESS trial is aimed to evaluate the clinical effectiveness of a novel ddPCR assay compared with standard practice. Methods PROGRESS is a multicenter, open-label, pragmatic randomized controlled trial (pRCT) set in ten hospitals, including departments of infectious disease and intensive care units. In this study, a total of 2292 patients with suspected sepsis will be randomly assigned to two arms: the ddPCR group and the control group with a ratio of 3:1. The primary outcome is the diagnostic efficacy, that is, the sensitivity and specificity of the ddPCR assay compared with the synchronous blood culture. Secondary outcomes include the mortality rates and the mean Sequential Organ Failure Assessment (SOFA) score at follow-up time points, the length of stay in the hospital, the time to directed antimicrobial therapy, duration of broad-spectrum antibiotic use, and the EQ-5D-5L score on day 90. Discussion It is the first multicenter pragmatic RCT to explore the diagnostic efficacy and clinical impact of the ddPCR assay in patients with suspected sepsis, taking advantage of both RCT’s ability to establish causality and the feasibility of pragmatic approaches in real-world studies (RWS). This trial will help us to get a comprehensive view of the assay’s capacity for precise diagnosis and treatment of sepsis. It has the potential to monitor the pathogen load change and to guide the antimicrobial therapy, making a beneficial impact on the prognosis of sepsis patients. Trial registration: ClinicalTrial.gov, NCT05190861. Registered January 13, 2022—‘Retrospectively registered’, https://clinicaltrials.gov/ct2/show/NCT05190861.
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Affiliation(s)
- Yuanhan Zhao
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Ke Lin
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Haocheng Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Guanmin Yuan
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China
| | - Yanliang Zhang
- Department of Infectious Diseases, The Nanjing Hospital of Chinese Medicine, Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Jingye Pan
- Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Liang Hong
- Department of Infectious Diseases, Ruian People's Hospital, Ruian, 325200, China
| | - Yan Huang
- Department of Infectious Diseases, Xiangya Hospital Central South University, No. 87 Xiangya Road, Changsha, 410000, Hunan, China
| | - Ying Ye
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Lisu Huang
- Department of Infectious Diseases, Xinhua Children's Hospital, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaohua Chen
- Department of Infectious Diseases, Shanghai Sixth Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Jun Liu
- Department of Laboratory, Wuxi No. 5 People's Hospital Affiliated to Nantong University, Wuxi, Jiangsu, China
| | - Xiang Li
- Department of Critical Care Medicine, Minhang Hospital, Fudan University, No. 39, Xinling Road, Minhang District, Shanghai, 201199, China
| | - Xiaoju He
- Department of Infectious Diseases, The Nanjing Hospital of Chinese Medicine, Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Qiaoyan Yue
- Department of Infectious Diseases, The Nanjing Hospital of Chinese Medicine, Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Hong Zhang
- Department of Infectious Diseases, The Nanjing Hospital of Chinese Medicine, Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Aiming Zhou
- Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yangyang Zhuang
- Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jie Chen
- Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Caixia Wu
- Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wei Zhou
- Department of Intensive Care Unit, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Fujing Cai
- Department of Infectious Diseases, Ruian People's Hospital, Ruian, 325200, China
| | - Shengguo Zhang
- Department of Infectious Diseases, Ruian People's Hospital, Ruian, 325200, China
| | - Liang Li
- Department of Infectious Diseases, Xiangya Hospital Central South University, No. 87 Xiangya Road, Changsha, 410000, Hunan, China
| | - Shaling Li
- Department of Infectious Diseases, Xiangya Hospital Central South University, No. 87 Xiangya Road, Changsha, 410000, Hunan, China
| | - Tingting Bian
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jiabin Li
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jun Yin
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zhengshang Ruan
- Department of Infectious Diseases, Xinhua Children's Hospital, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shanshan Xu
- Department of Infectious Diseases, Xinhua Children's Hospital, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Zhang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital Affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, 200092, China
| | - Jie Chen
- Department of Infectious Diseases, Shanghai Sixth Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Ying Zhang
- Department of Infectious Diseases, Wuxi No. 5 People's Hospital, Wuxi, Jiangsu, China
| | - Jun Han
- Department of Infectious Diseases, Wuxi No. 5 People's Hospital, Wuxi, Jiangsu, China
| | - Tingting Su
- Department of Infectious Diseases, Wuxi No. 5 People's Hospital, Wuxi, Jiangsu, China
| | - Fan Tu
- Department of Infectious Diseases, Wuxi No. 5 People's Hospital, Wuxi, Jiangsu, China
| | - Lijing Jiang
- Department of Critical Care Medicine, Minhang Hospital, Fudan University, No. 39, Xinling Road, Minhang District, Shanghai, 201199, China
| | - Chen Lei
- Department of Critical Care Medicine, Minhang Hospital, Fudan University, No. 39, Xinling Road, Minhang District, Shanghai, 201199, China
| | - Qiu Du
- Department of Pharmacy, The Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Jingwen Ai
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China.
| | - Wenhong Zhang
- Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, Huashan Hospital, Fudan University, Shanghai, China. .,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China. .,Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China.
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11
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Hart CR, McLendon PM, Naik RR. Dealing with a Pandemic: Emerging Tools, Solutions, and Challenges. Health Secur 2022; 20:109-115. [PMID: 35021893 DOI: 10.1089/hs.2021.0145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As a result of the COVID-19 pandemic, nations across the globe have responded by attempting to understand how the virus was spreading in their communities, in order to isolate cases, reduce morbidity and mortality, and avoid overwhelming healthcare facilities. In this article, we describe the global response to tracking the virus, and discuss new technological advances in molecular testing that have been deployed and developed to track and mitigate COVID-19. We also discuss how the successes and failures observed in the COVID-19 pandemic can be extrapolated to improve our ability to respond to the next pandemic.
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Affiliation(s)
- Corey R Hart
- Corey R. Hart, PhD, is a Senior Physiologist/Technical Integration Manager and Rajesh R. Naik, PhD, is Chief Scientist; both in the 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH. Patrick M. McLendon, PhD, is a Senior Scientist/Senior Technical Program Manager, Integrative Health and Performance Sciences Division, UES, Inc., Dayton, OH. The views expressed are those of the authors and do not reflect the official guidance or position of the United States Government, the Department of Defense or of the United States Air Force
| | - Patrick M McLendon
- Corey R. Hart, PhD, is a Senior Physiologist/Technical Integration Manager and Rajesh R. Naik, PhD, is Chief Scientist; both in the 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH. Patrick M. McLendon, PhD, is a Senior Scientist/Senior Technical Program Manager, Integrative Health and Performance Sciences Division, UES, Inc., Dayton, OH. The views expressed are those of the authors and do not reflect the official guidance or position of the United States Government, the Department of Defense or of the United States Air Force
| | - Rajesh R Naik
- Corey R. Hart, PhD, is a Senior Physiologist/Technical Integration Manager and Rajesh R. Naik, PhD, is Chief Scientist; both in the 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson Air Force Base, OH. Patrick M. McLendon, PhD, is a Senior Scientist/Senior Technical Program Manager, Integrative Health and Performance Sciences Division, UES, Inc., Dayton, OH. The views expressed are those of the authors and do not reflect the official guidance or position of the United States Government, the Department of Defense or of the United States Air Force
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12
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Mandal S, Khanna K, Johnson-Buck A, Walter NG. A guide to accelerated direct digital counting of single nucleic acid molecules by FRET-based intramolecular kinetic fingerprinting. Methods 2022; 197:63-73. [PMID: 34182140 DOI: 10.1016/j.ymeth.2021.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 01/03/2023] Open
Abstract
Cell-free nucleic acids (cfNAs) such as short non-coding microRNA (miRNA) and circulating tumor DNA (ctDNA) that reside in bodily fluids have emerged as potential cancer biomarkers. Methods for the rapid, highly specific, and sensitive monitoring of cfNAs in biofluids have, therefore, become increasingly attractive as clinical diagnosis tools. As a next generation technology, we provide a practical guide for an amplification-free, single molecule Förster resonance energy transfer (smFRET)-based kinetic fingerprinting approach termed intramolecular single molecule recognition through equilibrium Poisson sampling, or iSiMREPS, for the rapid detection and counting of miRNA and mutant ctDNA with virtually unlimited specificity and single molecule sensitivity. iSiMREPS utilizes a pair of fluorescent detection probes, wherein one probe immobilizes the target molecules on the surface, and the other probe transiently and reversibly binds to the target to generate characteristic time-resolved fingerprints as smFRET signal that are detected in a total internal reflection fluorescence microscope. Analysis of these kinetic fingerprints enables near-perfect discrimination between specific binding to target molecules and nonspecific background binding. By accelerating kinetic fingerprinting using the denaturant formamide and reducing background signals by removing target-less probes from the surface via toehold-mediated strand displacement, iSiMREPS has been demonstrated to count miR-141 and EGFR exon 19 deletion ctDNA molecules with a limit of detection (LOD) of ~1 and 3 fM, respectively, as well as mutant allele fractions as low as 0.0001%, during a standard acquisition time of only ~10 s per field of view. In this review, we provide a detailed roadmap for implementing iSiMREPS more broadly in research and clinical diagnostics, combining rapid analysis, high specificity, and high sensitivity.
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13
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Cassedy A, Della Bartola M, Parle-McDermott A, Mullins E, O'Kennedy R. A one-step reverse transcription recombinase polymerase amplification assay for lateral flow-based visual detection of PVY. Anal Biochem 2021; 642:114526. [PMID: 34922917 DOI: 10.1016/j.ab.2021.114526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 12/07/2021] [Accepted: 12/11/2021] [Indexed: 12/12/2022]
Abstract
Potato virus Y (PVY) is an abundant and damaging virus which reduces crop yield and marketability. Accurate detection of this economically important virus both in-field and in seed potato is considered essential in the control of PVY spread. Current detection methods are focused on immunodetection and PCR-based methods, however, identification of PVY through isothermal amplification is a promising avenue for developing accessible, on-site diagnostics with quick turnaround times. In this work, a rapid recombinase polymerase amplification assay was developed which could readily amplify PVY nucleic acids with good sensitivity and specificity. Additionally, this assay was shown to be capable of amplification directly from RNA in a one-step amplification process, without the need for prior reverse transcription. The assay was coupled with lateral flow technology to provide a rapid visual confirmation of amplification. This nucleic-acid lateral flow immunoassay could feasibly be employed in-field, or at any location where testing is required, to aid in the detection and control of PVY.
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Affiliation(s)
- Arabelle Cassedy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland.
| | | | | | - Ewen Mullins
- Crop Science Department, Teagasc, Oak Park, Carlow, Ireland
| | - Richard O'Kennedy
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland; Hamad Bin Khalifa University, Education City, Doha, Qatar; Qatar Foundation, Education City, Doha, Qatar.
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14
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Bach K, Edel B, Höring S, Bartoničkova L, Glöckner S, Löffler B, Bahrs C, Rödel J. Performance of the eazyplex® BloodScreen GN as a simple and rapid molecular test for identification of Gram-negative bacteria from positive blood cultures. Eur J Clin Microbiol Infect Dis 2021; 41:489-494. [PMID: 34807364 PMCID: PMC8831353 DOI: 10.1007/s10096-021-04383-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/16/2021] [Indexed: 12/18/2022]
Abstract
The LAMP-based eazyplex® BloodScreen GN was evaluated for the detection of frequent Gram-negatives directly from positive blood culture (BC) bottles. A total of 449 BCs were analyzed. Sensitivities and specificities were 100% and 100% for Escherichia coli, 95.7% and 100% for Klebsiella pneumoniae, 100% and 100% for blaCTX-M, 100% and 100% for Klebsiella oxytoca, 100% and 99% for Proteus mirabilis, and 100% and 99.8% for Pseudomonas aeruginosa, respectively. The time to result ranged from 8 to 16 min, plus about 6 min for sample preparation. The eazyplex® BloodScreen GN is a reliable molecular assay for rapid BC testing.
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Affiliation(s)
- Katharina Bach
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Birgit Edel
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Steffen Höring
- Division of Infection Control and Infectious Diseases, RWTH Aachen University Hospital, Aachen, Germany
| | - Lucie Bartoničkova
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Stefan Glöckner
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Christina Bahrs
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Friedrich Schiller University, Jena, Germany
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Jürgen Rödel
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
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15
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Åkerlund A, Petropoulos A, Malmros K, Tängdén T, Giske CG. Blood culture diagnostics: a Nordic multicentre survey comparison of practices in clinical microbiology laboratories. Clin Microbiol Infect 2021; 28:731.e1-731.e7. [PMID: 34537364 DOI: 10.1016/j.cmi.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 08/17/2021] [Accepted: 09/04/2021] [Indexed: 11/19/2022]
Abstract
OBJECTIVES Accurate and rapid microbiological diagnostics are crucial to tailor treatment and improve outcomes in patients with severe infections. This study aimed to assess blood culture diagnostics in the Nordic countries and to compare them with those of a previous survey conducted in Sweden in 2013. METHODS An online questionnaire was designed and distributed to the Nordic clinical microbiology laboratories (CMLs) (n = 76) in January 2018. RESULTS The response rate was 64% (49/76). Around-the-clock incubation of blood cultures (BCs) was supported in 82% of the CMLs (40/49), although in six of these access to the incubators around the clock was not given to all of the cabinets in the catchment area, and 41% of the sites (20/49) did not assist with satellite incubators. Almost half (49%, 24/49) of the CMLs offered opening hours for ≥10 h during weekdays, more commonly in CMLs with an annual output ≥30 000 BCs. Still, positive BCs were left unprocessed for 60-70% of the day due to restrictive opening hours. Treatment advice was given by 23% of CMLs (11/48) in ≥75% of the phone contacts. Rapid analyses (species identification and susceptibility testing with short incubation), performed on aliquots from positive cultures, were implemented in 18% of CMLs (9/49). Compared to 2013, species identification from subcultured colonies (<6 h) had become more common. CONCLUSIONS CMLs have taken action to improve aspects of BC diagnostics, implementing satellite incubators, rapid species identification and susceptibility testing. However, the limited opening hours and availability of clinical microbiologists are confining the advantages of these changes.
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Affiliation(s)
- Anna Åkerlund
- Division of Clinical Microbiology, Laboratory Medicine, Jönköping, Region Jönköping County, and Department of Clinical and Experimental Medicine, Linköping University, Sweden; Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University Hospital, Linköping, Sweden.
| | - Alexandros Petropoulos
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Malmros
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Thomas Tängdén
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Christian G Giske
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden; Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
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Abstract
Point-of-care (POC) or near patient testing for infectious diseases is a rapidly expanding space that is part of an ongoing effort to bring care closer to the patient. Traditional POC tests were known for their limited utility, but advances in technology have seen significant improvements in performance of these assays. The increasing promise of these tests is also coupled with their increasing complexity, which requires the oversight of qualified laboratory-trained personnel.
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Affiliation(s)
- Linoj Samuel
- Clinical Microbiology, Department of Pathology and Laboratory Medicine, Henry Ford Hospital, 2799 West Grand Boulevard, Detroit, MI 48202, USA.
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17
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Holma T, Torvikoski J, Friberg N, Nevalainen A, Tarkka E, Antikainen J, Martelin JJ. Rapid molecular detection of pathogenic microorganisms and antimicrobial resistance markers in blood cultures: evaluation and utility of the next-generation FilmArray Blood Culture Identification 2 panel. Eur J Clin Microbiol Infect Dis 2021; 41:363-371. [PMID: 34350523 PMCID: PMC8831274 DOI: 10.1007/s10096-021-04314-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/09/2021] [Indexed: 11/30/2022]
Abstract
Rapid detection of pathogens causing bloodstream infections (BSI) directly from positive blood cultures is of highest importance in order to enable an adequate and timely antimicrobial therapy. In this study, the utility and performance of a recently launched next-generation fully automated test system, the Biofire FilmArray® Blood Culture Identification 2 (BCID2) panel, was evaluated using a set of 103 well-characterized microbial isolates including 29 antimicrobial resistance genes and 80 signal-positive and 23 signal-negative clinical blood culture samples. The results were compared to culture-based reference methods, MALDI-TOF, and/or 16S rDNA sequencing. Of the clinical blood culture samples, 68 were monomicrobial (85.0%) and 12 polymicrobial (15.0%). Six samples contained ESBL (blaCTX-M), two MRSA (mecA), and three MRSE (mecA) isolates. In overall, the FilmArray BCID2 panel detected well on-panel targets and resistance markers from mono- and polymicrobial samples. However, one Klebsiella aerogenes and one Bacteroides ovatus were undetected, and the assay falsely reported one Shigella flexneri as Escherichia coli. Hence, the sensitivity and specificity for detecting microbial species were 98.8% (95%CI, 95.8–99.9%) and 99.9% (95%CI, 99.8–99.9%), respectively. The sensitivity and specificity for detecting of resistance gene markers were 100%. The results were available within 70 min from signal-positive blood cultures with minimal hands-on time. In conclusion, the BCID2 test allows reliable and simplified detection of a vast variety of clinically relevant microbes causing BSI and the most common antimicrobial resistance markers present among these isolates.
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Affiliation(s)
- Tanja Holma
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
| | - Jukka Torvikoski
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Nathalie Friberg
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Annika Nevalainen
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Eveliina Tarkka
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jenni Antikainen
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jari J Martelin
- HUS Diagnostic Center, HUSLAB, Department of Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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18
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van der Schalk TE, Coppens J, Timbermont L, Turlej-Rogacka A, Van Heirstraeten L, Berkell M, Yu L, Lammens C, Xavier BB, Matheeussen V, Ieven M, McCarthy M, Jorens PG, Ruzin A, Esser MT, Kumar-Singh S, Goossens H, Malhotra-Kumar S. Evaluation of GeneXpert PA assay compared to genomic and (semi-)quantitative culture methods for direct detection of Pseudomonas aeruginosa in endotracheal aspirates. Antimicrob Resist Infect Control 2021; 10:110. [PMID: 34301343 DOI: 10.1186/s13756-021-00978-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/08/2021] [Indexed: 01/02/2023] Open
Abstract
Introduction Pseudomonas aeruginosa is a common cause of ventilator-associated pneumonia (VAP). Rapid and accurate detection of lower respiratory tract colonization and/or infection with P. aeruginosa may advise targeted preventive (antibody-based) strategies and antibiotic therapy. To investigate this, we compared semi-quantitative culture results from 80 endotracheal aspirates (ETA) collected from mechanically-ventilated patients, to two culture and two non-culture-based methods for detection of P. aeruginosa. Methods P. aeruginosa-positive (n = 40) and -negative (n = 40) ETAs from mechanically ventilated patients analyzed initally by (i) routine semi-quantitative culture, were further analyzed with (ii) quantitative culture on chromogenic ChromID P. aeruginosa and blood agar; (iii) enrichment in brain heart infusion broth followed by plating on blood agar and ChromID P. aeruginosa; (iv) O-antigen acetylase gene-based TaqMan qPCR; and (v) GeneXpert PA PCR assay. Results Of the 80 ETA samples included, one sample that was negative for P. aeruginosa by semi-quantitative culture was found to be positive by the other four methods, and was included in an “extended” gold standard panel. Based on this extended gold standard, both semi-quantitative culture and the GeneXpert PA assay showed 97.6% sensitivity and 100% specificity. The quantitative culture, enrichment culture and O-antigen acetylase gene-based TaqMan qPCR had a sensitivity of 97.6%, 89.5%, 92.7%, and a specificity of 97.4%, 100%, and 71.1%, respectively.
Conclusion This first evaluation of the GeneXpert PA assay with ETA samples found it to be as sensitive and specific as the routine, hospital-based semi-quantitative culture method. Additionally, the GeneXpert PA assay is easy to perform (hands-on time ≈ 5 min) and rapid (≈ 55 min assay time). The combination of the high sensitivity and high specificity together with the rapid acquisition of results makes the GeneXpert PA assay a highly recommended screening technique. Where this equipment is not available, semi-quantitative culture remains the most sensitive of the culture methods evaluated here for P. aeruginosa detection in ETA samples. Supplementary Information The online version contains supplementary material available at 10.1186/s13756-021-00978-9.
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Xie S, Zhang J, Chen H, Wang W, Wang P, Xie Q, Li T, Wan Z, Shao H, Qin A, Ye J. Development of colloidal gold-based test strip for rapid detection of serotype 4 fowl adenovirus. J Virol Methods 2021; 296:114231. [PMID: 34245789 DOI: 10.1016/j.jviromet.2021.114231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
The outbreaks of hepatitis-hydropericardium syndrome (HPS) caused by serotype 4 fowl adenovirus (FAdV-4) have spread from broilers to laying hens, breeders, geese and Cherry Valley duck, resulting in high economic losses to the poultry industry globally. In this study, a rapid colloidal gold test strip for detection of FAdV-4 was developed by using two monoclonal antibodies (mAbs) against the Fiber-2 of FAdV-4. Specificity analysis revealed that the test strip only reacted with FAdV-4, but not with other pathogens including different serotypes of fowl adenovirus and other avian pathogens tested. The limit of the detection (LOD) of the strip could reach as low as 0.1 μg/0.1 mL of GST-Fiber-2 protein and 1 × 105 TCID50/0.1 mL of FAdV-4, respectively. Moreover, the test strip could be efficiently applied in detecting tissue samples from diseased chickens with HPS. Comparison analysis further revealed that the test strip showed good compatibility with PCR assay for detection of virus isolates and clinical samples. In conclusion, our test strip provides an efficient on-site diagnostic method in a quick and convenient manner for detection of FAdV-4, especially in resource-limited areas.
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Affiliation(s)
- Songhua Xie
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Jianjun Zhang
- Sinopharm Yangzhou VAC Biological Engineering Co. Ltd, Yangzhou, Jiangsu, 225127, China
| | - Hongjun Chen
- Shanghai Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Weikang Wang
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Ping Wang
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Quan Xie
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Tuofan Li
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Zhimin Wan
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Hongxia Shao
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Aijian Qin
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China.
| | - Jianqiang Ye
- Key Laboratory of Jiangsu Preventive Veterinary Medicine, Key Laboratory for Avian Preventive Medicine, Ministry of Education, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, China; Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, Jiangsu, 225009, China.
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20
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Ng DHL, Sim MY, Huang HH, Sim JXY, Low JGH, Lim JKS. Feasibility and utility of facemask sampling in the detection of SARS-CoV-2 during an ongoing pandemic. Eur J Clin Microbiol Infect Dis 2021; 40:2489-2496. [PMID: 34224033 PMCID: PMC8256409 DOI: 10.1007/s10096-021-04302-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/28/2021] [Indexed: 12/18/2022]
Abstract
Easy access to screening for timely identification and isolation of infectious COVID-19 patients remains crucial in sustaining the international efforts to control COVID-19 spread. A major barrier limiting broad-based screening is the lack of a simple, rapid, and cost-effective COVID-19 testing method. We evaluated the feasibility and utility of facemask sampling in a cohort of 42 COVID-19-positive and 36 COVID-19-negative patients. We used a prototype of Steri-Strips™ (3 M) applied to the inner surface of looped surgical facemasks (Assure), which was worn by patients for a minimum wear time of 3 h, then removed and sent for SARS-CoV-2 PCR testing. Baseline demographics and symptomatology were also collected. Facemask sampling positivity was highest within the first 5 days of symptomatic presentation. Patients with nasopharyngeal and/or oropharyngeal swab SARS-CoV-2 PCR Ct values < 25.09 had SARS-CoV-2 detected on facemask sampling, while patients with Ct values ≥ 25.2 had no SARS-CoV-2 detected on facemask sampling. Facemask sampling can identify patients with COVID-19 during the early symptomatic phase or those with high viral loads, hence allowing timely identification and isolation of those with the highest transmission risk. Given the widespread use of facemasks, this method can potentially be easily applied to achieve broad-based, or even continuous, population screening.
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Affiliation(s)
- Dorothy Hui Lin Ng
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore.
| | - Mei Yi Sim
- Department of Urology, Singapore General Hospital, Singapore, Singapore
| | - Hong Hong Huang
- Department of Urology, Singapore General Hospital, Singapore, Singapore
| | - Jean Xiang Ying Sim
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore
| | - Jenny Guek Hong Low
- Department of Infectious Diseases, Singapore General Hospital, Singapore, Singapore.,Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Jay Kheng Sit Lim
- Department of Urology, Singapore General Hospital, Singapore, Singapore
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21
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Baldan R, Cliff PR, Burns S, Medina A, Smith GC, Batra R, Cerda A, Wilson R, Merrill T, Lewis SJ, Patel A, Jeyaratnam D, Wyncoll DL, Barrett N, Chand MA, Edgeworth JD. Development and evaluation of a nanopore 16S rRNA gene sequencing service for same day targeted treatment of bacterial respiratory infection in the intensive care unit. J Infect 2021; 83:167-74. [PMID: 34146598 DOI: 10.1016/j.jinf.2021.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 01/16/2023]
Abstract
OBJECTIVES Assess the feasibility and impact of nanopore-based 16S rRNA gene sequencing (Np16S) service on antibiotic treatment for acute severe pneumonia on the intensive care unit (ICU). METHODS Speciation and sequencing accuracy of Np16S on isolates with bioinformatics pipeline optimisation, followed by technical evaluation including quality checks and clinical-reporting criteria analysing stored respiratory samples using single-sample flow cells. Pilot service comparing Np16S results with all routine respiratory tests and impact on same-day antimicrobial prescribing. RESULTS Np16S correctly identified 140/167 (84%) isolates after 1h sequencing and passed quality control criteria including reproducibility and limit-of-detection. Sequencing of 108 stored respiratory samples showed concordance with routine culture in 80.5% of cases and established technical and clinical reporting criteria. A 10-week same-day pilot Np16S service analysed 45 samples from 37 patients with suspected community (n=15) or hospital acquired (n=30) pneumonia. Np16S showed concordance compared with all routine culture or molecular tests for 27 (82%) of 33 positive samples. It identified the causative pathogen in 32/33 (97%) samples and contributed to antimicrobial treatment changes for 30 patients (67%). CONCLUSIONS This study demonstrates feasibility of providing a routine same-day nanopore sequencing service that makes a significant contribution to early antibiotic prescribing for bacterial pneumonia in the ICU.
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22
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Peri AM, Stewart A, Hume A, Irwin A, Harris PNA. New Microbiological Techniques for the Diagnosis of Bacterial Infections and Sepsis in ICU Including Point of Care. Curr Infect Dis Rep 2021; 23:12. [PMID: 34149321 DOI: 10.1007/s11908-021-00755-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2021] [Indexed: 12/22/2022]
Abstract
Purpose of Review The aim of this article is to review current and emerging microbiological techniques that support the rapid diagnosis of bacterial infections in critically ill patients, including their performance, strengths and pitfalls, as well as available data evaluating their clinical impact. Recent Findings Bacterial infections and sepsis are responsible for significant morbidity and mortality in patients admitted to the intensive care unit and their management is further complicated by the increase in the global burden of antimicrobial resistance. In this setting, new diagnostic methods able to overcome the limits of traditional microbiology in terms of turn-around time and accuracy are highly warranted. We discuss the following broad themes: optimisation of existing culture-based methodologies, rapid antigen detection, nucleic acid detection (including multiplex PCR assays and microarrays), sepsis biomarkers, novel methods of pathogen detection (e.g. T2 magnetic resonance) and susceptibility testing (e.g. morphokinetic cellular analysis) and the application of direct metagenomics on clinical samples. The assessment of the host response through new “omics” technologies might also aid in early diagnosis of infections, as well as define non-infectious inflammatory states. Summary Despite being a promising field, there is still scarce evidence about the real-life impact of these assays on patient management. A common finding of available studies is that the performance of rapid diagnostic strategies highly depends on whether they are integrated within active antimicrobial stewardship programs. Assessing the impact of these emerging diagnostic methods through patient-centred clinical outcomes is a complex challenge for which large and well-designed studies are awaited.
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23
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Caméléna F, Poncin T, Dudoignon E, Salmona M, Le Goff J, Donay JL, Lafaurie M, Darmon M, Azoulay E, Plaud B, Mebazaa A, Dépret F, Jacquier H, Berçot B. Rapid identification of bacteria from respiratory samples of patients hospitalized in intensive care units, with FilmArray Pneumonia Panel Plus. Int J Infect Dis 2021; 108:568-573. [PMID: 34087488 DOI: 10.1016/j.ijid.2021.05.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022] Open
Abstract
OBJECTIVES This study aimed to evaluate the performance of FilmArray Pneumonia Panel Plus (FA-PP) for the detection of typical bacterial pathogens in respiratory samples from patients hospitalized in intensive care units (ICUs). METHODS FA-PP was implemented for clinical use in the microbiology laboratory in March 2020. A retrospective analysis on a consecutive cohort of adult patients hospitalized in ICUs between March 2020 and May 2020 was undertaken. The respiratory samples included sputum, blind bronchoalveolar lavage (BBAL) and protected specimen brush (PSB). Conventional culture and FA-PP were performed in parallel. RESULTS In total, 147 samples from 92 patients were analysed; 88% had coronavirus disease 2019 (COVID-19). At least one pathogen was detected in 46% (68/147) of samples by FA-PP and 39% (57/147) of samples by culture. The overall percentage agreement between FA-PP and culture results was 98% (93-100%). Bacteria with semi-quantitative FA-PP results ≥105 copies/mL for PSB samples, ≥106 copies/mL for BBAL samples and ≥107 copies/mL for sputum samples reached clinically significant thresholds for growth in 90%, 100% and 91% of cultures, respectively. FA-PP detected resistance markers, including mecA/C, blaCTX-M and blaVIM. The median turnaround time was significantly shorter for FA-PP than for culture. CONCLUSIONS FA-PP may constitute a faster approach to the diagnosis of bacterial pneumonia in patients hospitalized in ICUs.
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Affiliation(s)
- François Caméléna
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France
| | - Thibaut Poncin
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France
| | - Emmanuel Dudoignon
- Department of Anaesthesiology and Critical Care and Burns Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique - Hôpitaux de Paris, Paris, France; University of Paris, FHU PROMICE, INSERM 942, INI-CRCT Network, Paris, France
| | - Maud Salmona
- University of Paris, Inserm U976, Insight team, F-75010, Paris France; Department of Virology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jérôme Le Goff
- University of Paris, Inserm U976, Insight team, F-75010, Paris France; Department of Virology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jean-Luc Donay
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Matthieu Lafaurie
- Department of Infectious Disease, Saint-Louis-Lariboisière Hospital Group, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Michael Darmon
- Medical Intensive Care Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique - Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1153, Centre of Epidemiology and Biostatistics, ECSTRA Team, Paris, France
| | - Elie Azoulay
- Medical Intensive Care Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique - Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1153, Centre of Epidemiology and Biostatistics, ECSTRA Team, Paris, France
| | - Benoît Plaud
- Department of Anaesthesiology and Critical Care and Burns Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique - Hôpitaux de Paris, Paris, France; University of Paris, FHU PROMICE, INSERM 942, INI-CRCT Network, Paris, France
| | - Alexandre Mebazaa
- Department of Anaesthesiology and Critical Care and Burns Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique - Hôpitaux de Paris, Paris, France; University of Paris, FHU PROMICE, INSERM 942, INI-CRCT Network, Paris, France
| | - François Dépret
- Department of Anaesthesiology and Critical Care and Burns Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique - Hôpitaux de Paris, Paris, France; University of Paris, FHU PROMICE, INSERM 942, INI-CRCT Network, Paris, France
| | - Hervé Jacquier
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France
| | - Béatrice Berçot
- Department of Bacteriology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France.
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24
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Anderson M, Holzmayer V, Vallari A, Taylor R, Moy J, Cloherty G. Expanding access to SARS-CoV-2 IgG and IgM serologic testing using fingerstick whole blood, plasma, and rapid lateral flow assays. J Clin Virol 2021; 141:104855. [PMID: 34144453 PMCID: PMC8111886 DOI: 10.1016/j.jcv.2021.104855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 12/31/2022]
Abstract
Serologic testing for SARS-CoV-2 antibodies can be used to confirm diagnosis, estimate seroprevalence, screen convalescent plasma donors, and assess vaccine efficacy. Dried blood spot (DBS) samples have been used for serology testing of various diseases in resource-limited settings. We examined the use of DBS samples and capillary blood (fingerstick) plasma collected in Microtainer tubes for SARS-CoV-2 testing with the automated Abbott ARCHITECT™ SARS-CoV-2 IgG and IgM assays and use of venous whole blood with a prototype PANBIO™ rapid point-of-care lateral flow SARS-CoV-2 IgG assay. The ARCHITECT™ SARS-CoV-2 IgG assay was initially optimized for use with DBS, venous and capillary plasma, and venous whole blood collected from patients with symptoms and PCR-confirmed COVID-19 and negative asymptomatic controls. Linearity and reproducibility was confirmed with 3 contrived DBS samples, along with sample stability and signal recovery after 14 days. ARCHITECT™ SARS-CoV-2 IgG and IgM assay results showed high concordance between fingerstick DBS and venous DBS samples, and between fingerstick DBS and venous whole blood samples (n = 61). Fingerstick plasma collected in Microtainer tubes (n = 109) showed 100% concordant results (R2=0.997) with matched patient venous plasma on the ARCHITECT™ SARS-CoV-2 IgG assay. High concordance of assay results (92.9% positive, 100% negative) was also observed for the PANBIO™ SARS-CoV-2 IgG assay compared to the ARCHITECT™ SARS-CoV-2 IgG assay run with matched venous plasma (n = 61). Fingerstick DBS and plasma samples are easy and inexpensive to collect and, along with the use of rapid point-of-care testing platforms, will expand access to SARS-CoV-2 serology testing, particularly in resource-limited areas.
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Affiliation(s)
- Mark Anderson
- Abbott Laboratories, Abbott Diagnostics Division, 100 Abbott Park Road, Bldg. AP20, Abbott Park, IL 60064-3500, United States
| | - Vera Holzmayer
- Abbott Laboratories, Abbott Diagnostics Division, 100 Abbott Park Road, Bldg. AP20, Abbott Park, IL 60064-3500, United States
| | - Ana Vallari
- Abbott Laboratories, Abbott Diagnostics Division, 100 Abbott Park Road, Bldg. AP20, Abbott Park, IL 60064-3500, United States
| | - Russell Taylor
- Abbott Laboratories, Abbott Diagnostics Division, 100 Abbott Park Road, Bldg. AP20, Abbott Park, IL 60064-3500, United States
| | - James Moy
- Rush University Medical Center, Chicago, Illinois, United States
| | - Gavin Cloherty
- Abbott Laboratories, Abbott Diagnostics Division, 100 Abbott Park Road, Bldg. AP20, Abbott Park, IL 60064-3500, United States.
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25
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Goodlet KJ, Tan E, Knutson L, Nailor MD. Impact of the FilmArray meningitis/encephalitis panel on antimicrobial duration among patients with suspected central nervous system infection. Diagn Microbiol Infect Dis 2021; 100:115394. [PMID: 34052576 DOI: 10.1016/j.diagmicrobio.2021.115394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/22/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
Ten controlled studies evaluated antimicrobial use following implementation of the FilmArray meningitis and encephalitis panel versus usual care. Only one-half of studies identified significant reductions in antibiotic duration, with 8/10 reporting modest reductions for acyclovir. Coupling the FilmArray meningitis and encephalitis panel with interventions by antimicrobial stewardship programs may help enhance its clinical impact.
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Affiliation(s)
- Kellie J Goodlet
- Department of Pharmacy Practice, Midwestern University College of Pharmacy, Glendale, AZ, USA.
| | - Elaine Tan
- Department of Pharmacy Practice, Midwestern University College of Pharmacy, Glendale, AZ, USA
| | - Lindsey Knutson
- Department of Pharmacy Practice, Midwestern University College of Pharmacy, Glendale, AZ, USA
| | - Michael D Nailor
- Department of Pharmacy Services, St. Joseph's Hospital and Medical Center, Phoenix, AZ, USA
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26
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Avershina E, Sharma P, Taxt AM, Singh H, Frye SA, Paul K, Kapil A, Naseer U, Kaur P, Ahmad R. AMR-Diag: Neural network based genotype-to-phenotype prediction of resistance towards β-lactams in Escherichia coli and Klebsiella pneumoniae. Comput Struct Biotechnol J 2021; 19:1896-1906. [PMID: 33897984 PMCID: PMC8060595 DOI: 10.1016/j.csbj.2021.03.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/15/2021] [Accepted: 03/23/2021] [Indexed: 12/11/2022] Open
Abstract
Antibiotic resistance poses a major threat to public health. More effective ways of the antibiotic prescription are needed to delay the spread of antibiotic resistance. Employment of sequencing technologies coupled with the use of trained neural network algorithms for genotype-to-phenotype prediction will reduce the time needed for antibiotic susceptibility profile identification from days to hours. In this work, we have sequenced and phenotypically characterized 171 clinical isolates of Escherichia coli and Klebsiella pneumoniae from Norway and India. Based on the data, we have created neural networks to predict susceptibility for ampicillin, 3rd generation cephalosporins and carbapenems. All networks were trained on unassembled data, enabling prediction within minutes after the sequencing information becomes available. Moreover, they can be used both on Illumina and MinION generated data and do not require high genome coverage for phenotype prediction. We cross-checked our networks with previously published algorithms for genotype-to-phenotype prediction and their corresponding datasets. Besides, we also created an ensemble of networks trained on different datasets, which improved the cross-dataset prediction compared to a single network. Additionally, we have used data from direct sequencing of spiked blood cultures and found that AMR-Diag networks, coupled with MinION sequencing, can predict bacterial species, resistome, and phenotype as fast as 1–8 h from the sequencing start. To our knowledge, this is the first study for genotype-to-phenotype prediction: (1) employing a neural network method; (2) using data from more than one sequencing platform; and (3) utilizing sequence data from spiked blood cultures.
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Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317 Hamar, Norway
| | - Priyanka Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Arne M Taxt
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317 Hamar, Norway.,Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956, Nydalen, 0424 Oslo, Norway
| | - Harpreet Singh
- Informatics, System and Research Management, Indian Council of Medical Research, New Delhi, India
| | - Stephan A Frye
- Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, PB 4956, Nydalen, 0424 Oslo, Norway
| | - Kolin Paul
- Department of Computer Science & Engineering, IIT Delhi, New Delhi, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Umaer Naseer
- Department of Zoonotic, Food- and Waterborne Infections, 0213 Oslo, Norwegian Institute of Public Health, Oslo, Norway
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Holsetgata 22, 2317 Hamar, Norway.,Institute of Clinical Medicine, Faculty of Health Sciences, UiT - The Arctic University of Norway, Hansine Hansens veg 18, 9019 Tromsø, Norway
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27
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Stokes W, Berenger BM, Portnoy D, Scott B, Szelewicki J, Singh T, Venner AA, Turnbull L, Pabbaraju K, Shokoples S, Wong AA, Gill K, Guttridge T, Proctor D, Hu J, Tipples G. Clinical performance of the Abbott Panbio with nasopharyngeal, throat, and saliva swabs among symptomatic individuals with COVID-19. Eur J Clin Microbiol Infect Dis 2021; 40:1721-1726. [PMID: 33742322 PMCID: PMC7979467 DOI: 10.1007/s10096-021-04202-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/16/2021] [Indexed: 11/26/2022]
Abstract
SARS-CoV-2 antigen tests used at the point-of-care, such as the Abbott Panbio, have great potential to help combat the COVID-19 pandemic. The Panbio is Health Canada approved for the detection of SARS-CoV-2 in symptomatic individuals within the first 7 days of COVID-19 symptom onset(s). Symptomatic adults recently diagnosed with COVID-19 in the community were recruited into the study. Paired nasopharyngeal (NP), throat, and saliva swabs were collected, with one paired swab tested immediately with the Panbio, and the other transported in universal transport media and tested using real-time reverse-transcriptase polymerase chain reaction (RT-PCR). We also prospectively evaluated results from assessment centers within the community. For those individuals, an NP swab was collected for Panbio testing and paired with RT-PCR results from parallel NP or throat swabs. One hundred and forty-five individuals were included in the study. Collection of throat and saliva was stopped early due to poorer performance (throat sensitivity 57.7%, n=61, and saliva sensitivity 2.6%, n=41). NP swab sensitivity was 87.7% [n=145, 95% confidence interval (CI) 81.0–92.7%]. There were 1641 symptomatic individuals tested by Panbio in assessment centers with 268/1641 (16.3%) positive for SARS-CoV-2. There were 37 false negatives and 2 false positives, corresponding to a sensitivity and specificity of 86.1% [95% CI 81.3–90.0%] and 99.9% [95% CI 99.5–100.0%], respectively. The Panbio test reliably detects most cases of SARS-CoV-2 from adults in the community setting presenting within 7 days of symptom onset using nasopharyngeal swabs. Throat and saliva swabs are not reliable specimens for the Panbio.
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Affiliation(s)
- William Stokes
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Alberta, Canada.
- Department of Pathology and Laboratory Medicine, University of Alberta, Edmonton, Alberta, Canada.
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
| | - Byron M Berenger
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Alberta, Canada
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Danielle Portnoy
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Brittney Scott
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jonas Szelewicki
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Takshveer Singh
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Allison A Venner
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Alberta, Canada
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - LeeAnn Turnbull
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Alberta, Canada
| | - Kanti Pabbaraju
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Alberta, Canada
| | - Sandy Shokoples
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Alberta, Canada
| | - Anita A Wong
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Alberta, Canada
| | - Kara Gill
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Alberta, Canada
| | - Tracy Guttridge
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Alberta, Canada
| | - Dustin Proctor
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Alberta, Canada
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jia Hu
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
- Public Health, Alberta Health Services, Alberta, Canada
| | - Graham Tipples
- Alberta Public Health Laboratory, Alberta Precision Laboratories, Alberta, Canada
- Department of Pathology and Laboratory Medicine, University of Alberta, Edmonton, Alberta, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
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28
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Howson ELA, Kidd SP, Armson B, Goring A, Sawyer J, Cassar C, Cross D, Lewis T, Hockey J, Rivers S, Cawthraw S, Banyard A, Anderson P, Rahou S, Andreou M, Morant N, Clark D, Walsh C, Laxman S, Houghton R, Slater-Jefferies J, Costello P, Brown I, Cortes N, Godfrey KM, Fowler VL. Preliminary optimisation of a simplified sample preparation method to permit direct detection of SARS-CoV-2 within saliva samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 2021; 289:114048. [PMID: 33358911 PMCID: PMC7750029 DOI: 10.1016/j.jviromet.2020.114048] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/28/2020] [Accepted: 12/12/2020] [Indexed: 11/15/2022]
Abstract
We describe the optimisation of a simplified sample preparation method which permits rapid and direct detection of SARS-CoV-2 RNA within saliva, using reverse-transcription loop-mediated isothermal amplification (RT-LAMP). Treatment of saliva samples prior to RT-LAMP by dilution 1:1 in Mucolyse™, followed by dilution in 10 % (w/v) Chelex© 100 Resin and a 98 °C heat step for 2 min enabled detection of SARS-CoV-2 RNA in positive saliva samples. Using RT-LAMP, SARS-CoV-2 RNA was detected in as little as 05:43 min, with no amplification detected in 3097 real-time reverse transcription PCR (rRT-PCR) negative saliva samples from staff tested within a service evaluation study, or for other respiratory pathogens tested (n = 22). Saliva samples can be collected non-invasively, without the need for skilled staff and can be obtained from both healthcare and home settings. Critically, this approach overcomes the requirement for, and validation of, different swabs and the global bottleneck in obtaining access to extraction robots and reagents to enable molecular testing by rRT-PCR. Such testing opens the possibility of public health approaches for effective intervention during the COVID-19 pandemic through regular SARS-CoV-2 testing at a population scale, combined with isolation and contact tracing.
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Affiliation(s)
- Emma L A Howson
- GeneSys Biotech Limited, Camberley, Surrey, UK; The Pirbright Institute, Ash Road, Woking, Surrey, UK
| | - Stephen P Kidd
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK.
| | - Bryony Armson
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK; vHive, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Alice Goring
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK
| | - Jason Sawyer
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Claire Cassar
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - David Cross
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Tom Lewis
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Jess Hockey
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | | | | | - Paul Anderson
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Sabah Rahou
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | - Nick Morant
- GeneSys Biotech Limited, Camberley, Surrey, UK
| | | | | | | | - Rebecca Houghton
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK
| | | | - Paula Costello
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK
| | - Ian Brown
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Nicholas Cortes
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK; Gibraltar Health Authority, Gibraltar, UK
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK; NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton, UK
| | - Veronica L Fowler
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK
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Bianco G, Boattini M, Iannaccone M, Pastrone L, Bondi A, Peradotto M, Cavallo R, Costa C. Integrating rapid diagnostics in Gram-negative bloodstream infections of patients colonized by carbapenemase-producing Enterobacterales. J Hosp Infect 2021; 110:84-8. [PMID: 33539936 DOI: 10.1016/j.jhin.2021.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 12/25/2022]
Abstract
We implemented a fast-track diagnostic approach for Gram-negative bloodstram infections (BSIs) among carbapenemase-producing Enterobacterales (CPE) carriers. Within a large cohort of patients with CPE rectal carriage, 18.1% developed Gram-negative BSIs, of which 69.5% were caused by CPE. Direct matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis provided reliable identification in 97% and 53.8% of monomicrobical blood cultures positive to Enterobacterales and non-fermenting Gram-negative species, respectively. Overall, sensitivity and specificity of NG-Test Carba 5 compared with the composite reference method after discrepant analysis were 100%, in polimicrobial blood cultures too. The combined use of direct MALDI-TOF MS and NG-Test Carba 5 assay might be a reliable and cost-effective tool for accelerating the laboratory diagnosis of CPE BSI in cohorts of high-risk patients such as CPE carriers.
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Steuber TD, Butler L, Sawyer A, Chappell R, Edwards J. Comparison of blood cultures versus T2 Candida Panel in management of candidemia at a large community hospital. Eur J Clin Microbiol Infect Dis 2021; 40:997-1001. [PMID: 33387121 DOI: 10.1007/s10096-020-04144-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 12/27/2020] [Indexed: 11/25/2022]
Abstract
The T2 Candida Panel (T2CP) has high sensitivity and specificity to detect candidemia. Its role in the diagnosis and management of candidemia compared to blood cultures (BC) remains unclear. The purpose of this study was to evaluate the T2CP versus BC in detecting and treating candidemia. A retrospective, observational cohort study was conducted to compare clinical outcomes in patients with candidemia identified by BC versus T2CP. Patients with a positive BC or T2CP for Candida spp. from January 2012 to August 2020 were grouped by initial method of detection (BC vs T2CP). Co-primary endpoints assessed included time to detection of candidemia and time to antifungal therapy. Key secondary endpoints included length of stay (LOS), ICU LOS, and mortality. One hundred sixty-three patients with a positive BC and 89 patients with a positive T2CP were included in the evaluation. The average time to detection of candidemia was significantly shorter in the T2CP group compared to BC group (9 vs 41 h, p < 0.001). The time to antifungal was also significantly shorter in the T2CP group compared to the BC group (4 vs 37 h, p < 0.001). However, LOS was significantly shorter in the BC positive group than the T2CP group with no difference in ICU LOS. There was no difference in in-hospital or 30-day mortality between the two groups. Of patients diagnosed with candidemia at our large community hospital, identification by T2CP led to faster detection and initiation of antifungal compared to blood cultures without improvement in LOS or mortality.
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Affiliation(s)
- Taylor D Steuber
- Department of Pharmacy Practice, Auburn University Harrison School of Pharmacy, 301 Governors Drive SW, Huntsville, AL, 35801, USA.
- Department of Pharmacy, Huntsville Hospital, 101 Sivley Road, Huntsville, AL, 35801, USA.
| | - Lauren Butler
- Department of Pharmacy, Huntsville Hospital, 101 Sivley Road, Huntsville, AL, 35801, USA
| | - Adam Sawyer
- Department of Pharmacy, Huntsville Hospital, 101 Sivley Road, Huntsville, AL, 35801, USA
| | - Rachel Chappell
- Department of Pharmacy, DCH Regional Medical Center, 809 University Boulevard East, Tuscaloosa, AL, 35401, USA
| | - Jonathan Edwards
- Department of Pharmacy, Huntsville Hospital, 101 Sivley Road, Huntsville, AL, 35801, USA
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Fowler VL, Armson B, Gonzales JL, Wise EL, Howson ELA, Vincent-Mistiaen Z, Fouch S, Maltby CJ, Grippon S, Munro S, Jones L, Holmes T, Tillyer C, Elwell J, Sowood A, de Peyer O, Dixon S, Hatcher T, Patrick H, Laxman S, Walsh C, Andreou M, Morant N, Clark D, Moore N, Houghton R, Cortes NJ, Kidd SP. A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection. J Infect 2021; 82:117-125. [PMID: 33271166 PMCID: PMC7703389 DOI: 10.1016/j.jinf.2020.10.039] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/04/2020] [Accepted: 10/07/2020] [Indexed: 12/23/2022]
Abstract
The COVID-19 pandemic has illustrated the importance of simple, rapid and accurate diagnostic testing. This study describes the validation of a new rapid SARS-CoV-2 RT-LAMP assay for use on extracted RNA or directly from swab offering an alternative diagnostic pathway that does not rely on traditional reagents that are often in short supply during a pandemic. Analytical specificity (ASp) of this new RT-LAMP assay was 100% and analytical sensitivity (ASe) was between 1 × 101 and 1 × 102 copies per reaction when using a synthetic DNA target. The overall diagnostic sensitivity (DSe) and specificity (DSp) of RNA RT-LAMP was 97% and 99% respectively, relative to the standard of care rRT-PCR. When a CT cut-off of 33 was employed, above which increasingly evidence suggests there is a low risk of patients shedding infectious virus, the diagnostic sensitivity was 100%. The DSe and DSp of Direct RT-LAMP (that does not require RNA extraction) was 67% and 97%, respectively. When setting CT cut-offs of ≤33 and ≤25, the DSe increased to 75% and 100%, respectively, time from swab-to-result, CT < 25, was < 15 min. We propose that RNA RT-LAMP could replace rRT-PCR where there is a need for increased sample throughput and Direct RT-LAMP as a near-patient screening tool to rapidly identify highly contagious individuals within emergency departments and care homes during times of increased disease prevalence ensuring negative results still get laboratory confirmation.
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Affiliation(s)
- Veronica L Fowler
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; Eco Animal Health, The Grange, 100 The High Street, London, UK
| | - Bryony Armson
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Jose L Gonzales
- Wageningen Bioveterinary Research (WBVR), PO Box 65, 8200 AB Lelystad, the Netherlands
| | - Emma L Wise
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Emma L A Howson
- GeneSys Biotech Limited, Camberley, Surrey, UK; The Pirbright Institute, Ash Road, Pirbright, Woking, UK
| | - Zoe Vincent-Mistiaen
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; Gibraltar Health Authority, Gibraltar, UK
| | - Sarah Fouch
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; School of Pharmacy and Biomedical Sciences, University of Portsmouth, UK
| | - Connor J Maltby
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Seden Grippon
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Simon Munro
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Lisa Jones
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Tom Holmes
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Claire Tillyer
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Joanne Elwell
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Amy Sowood
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Oliver de Peyer
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Sophie Dixon
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Thomas Hatcher
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Helen Patrick
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | | | | | | | - Nick Morant
- GeneSys Biotech Limited, Camberley, Surrey, UK
| | | | - Nathan Moore
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Rebecca Houghton
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Nicholas J Cortes
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; Gibraltar Health Authority, Gibraltar, UK
| | - Stephen P Kidd
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK.
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32
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Fiamanya S, Cipolla L, Prieto M, Stelling J. Exploring the value of MALDI-TOF MS for the detection of clonal outbreaks of Burkholderia contaminans. J Microbiol Methods 2020; 181:106130. [PMID: 33383044 DOI: 10.1016/j.mimet.2020.106130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 10/22/2022]
Abstract
BACKGROUND Molecular genetics has risen in both output and affordability to become the gold standard in diagnosis, however it is not yet available for most routine clinical microbiology due to cost and the level of skill it requires. Matrix assisted laser desorption/ionisation - time of flight mass spectrometry (MALDI-TOF MS) approaches may be useful in bridging the gap between low-resolution phenotypic methods and bulky genotypic methods in the goal of epidemiological source-typing of microbes. Burkholderia has been shown to be identifiable at the subspecies level using MALDI-TOF MS. There have not yet been studies assessing the ability of MALDI-TOF MS to source-type Burkholderia contaminans isolates into epidemiologically relevant outbreak clusters. METHODS 55 well-characterised B. contaminans isolates were used to create a panel for analysis of MALDI-TOF MS biomarker peaks and their relation to outbreak strains, location, source, patient, diagnosis and isolate genetics. Unsupervised clustering was performed and classification models were generated using biostatistical analysis software. RESULTS B. contaminans spectra derived from MALDI-TOF MS were of sufficiently high resolution to identify 100% of isolates. Unsupervised clustering methods showed poor evidence of spectra clustering by all characteristics measured. Classification algorithms were discriminatory, with Genetic Algorithm models showing 100% recognition capability for all outbreaks, the pulsed-field gel electrophoresis (PFGE) typeability model, and 96.63% recognition for the location model. A consistent peak at m/z of approximately 6943 was identified in all non-typeable strains but in none of the typeable strains. CONCLUSIONS MALDI-TOF MS successfully discriminates B. contaminans isolates into clonal, epidemiological clusters, and can recognise isolates non-typeable by PFGE. Further work should investigate this capability, and include peptide studies and genomic sequencing to identify individual proteins or genes responsible for this non-typeablity, particularly at the peak weight identified.
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Affiliation(s)
- Selali Fiamanya
- Oxford University Clinical Academic Graduate School, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom.
| | - Lucía Cipolla
- Servicio Bacteriología Especial, Instituto Nacional de Enfermedades Infecciosas 'Dr. C. G. Malbrán', Av Velez Sarsfield 563, 1281 Ciudad Autónoma de Buenos Aires, Argentina
| | - Mónica Prieto
- Servicio Bacteriología Especial, Instituto Nacional de Enfermedades Infecciosas 'Dr. C. G. Malbrán', Av Velez Sarsfield 563, 1281 Ciudad Autónoma de Buenos Aires, Argentina
| | - John Stelling
- Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School 25 Shattuck Street, Boston, MA 02115, USA
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Holma T, Antikainen J, Haiko J. Evaluation of three molecular carbapenemase tests: Eazyplex SuperBug complete B, Novodiag CarbaR+, and Amplidiag CarbaR+MCR. J Microbiol Methods 2020; 180:106105. [PMID: 33217483 DOI: 10.1016/j.mimet.2020.106105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Carbapenemase-producing Gram-negative bacilli, i.e., Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter, are of increased concern for the public health around the world. There is urgent need for rapid and accurate tests in order to provide correct treatment and to prevent bacterial spread in healthcare settings. METHODS The aim of this study was to evaluate three commercial multiplex carbapenemase tests with CE-IVD marking: Eazyplex SuperBug complete B (AmplexDiagnostics), Novodiag CarbaR+ (Mobidiag), and Amplidiag CarbaR+MCR (Mobidiag). All these tests recognize KPC, NDM, OXA-48/181 group, VIM, OXA-23 group, and OXA-24/40 group, and Novodiag CarbaR+ and Amplidiag CarbaR+MCR additionally recognize IMP, OXA-51 group (with promoter located within ISAbaI), OXA-58 group, and MCR, and Amplidiag CarbaR+MCR further recognizes GES (carbapenemase-type only). RESULTS The sensitivities and specificities of these tests with bacterial isolates were 100%. The sensitivity directly from clinical samples was 100%, but the specificity was lower, which is simply explained by the higher sensitivity of the molecular methods compared with culture method. CONCLUSIONS Overall, these CE-IVD marked tests provide a good alternative in the detection of carbapenemase-producing organisms.
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Affiliation(s)
- Tanja Holma
- Helsinki University and Helsinki University Hospital, HUSLAB, Department of Clinical Microbiology, Helsinki, Finland
| | - Jenni Antikainen
- Helsinki University and Helsinki University Hospital, HUSLAB, Department of Clinical Microbiology, Helsinki, Finland
| | - Johanna Haiko
- Helsinki University and Helsinki University Hospital, HUSLAB, Department of Clinical Microbiology, Helsinki, Finland.
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Ernst E, Wolfe P, Stahura C, Edwards KA. Technical considerations to development of serological tests for SARS-CoV-2. Talanta 2020; 224:121883. [PMID: 33379092 PMCID: PMC7654332 DOI: 10.1016/j.talanta.2020.121883] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/06/2020] [Accepted: 11/07/2020] [Indexed: 12/21/2022]
Abstract
The COVID-19 pandemic has had a devastating impact worldwide and has brought clinical assays both for acute diagnosis and prior exposure determination to the forefront. Serological testing intended for point-of-care or laboratory use can be used to determine more accurate individual and population assessments of prior exposure to SARS-CoV-2; improve our understanding of the degree to which immunity is conveyed to subsequent exposures; and quantify immune response to future vaccines. In response to this pandemic, initially more than 90 companies deployed serology assays to the U.S. market, many of which made overstated claims for their accuracy, regulatory approval status, and utility for intended purpose. The U.S. Food and Drug Administration subsequently instituted an Emergency Use Authorization (EUA) procedure requiring that manufacturers submit validation data, but allowing newly developed serological tests to be marketed without the usual approval process during this crisis. Although this rapid deployment was intended to benefit public health, the incomplete understanding of immune response to the virus and lack of assay vetting resulted in quality issues with some of these tests, and thus many were withdrawn after submission. Common assay platforms include lateral flow assays which can serve an important niche of low cost, rapid turnaround, and increased accessibility whereas established laboratory-based platforms based on ELISAs and chemiluminescence expand existing technologies to SARS-CoV-2 and can provide throughput and quantification capabilities. While most of the currently EUA assays rely on these well-established platforms, despite their apparent technical simplicity, there are numerous practical challenges both for manufacturers in developing and for end-users in running and interpreting such assays. Within are discussed technical challenges to serology development for SARS-CoV-2, with an emphasis on lateral flow assay technology.
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Affiliation(s)
- Emilie Ernst
- Department of Pharmaceutical Sciences School of Pharmacy and Pharmaceutical Sciences Binghamton University, Johnson City, NY, 13790, USA.
| | - Patricia Wolfe
- Department of Pharmaceutical Sciences School of Pharmacy and Pharmaceutical Sciences Binghamton University, Johnson City, NY, 13790, USA.
| | - Corrine Stahura
- Department of Pharmaceutical Sciences School of Pharmacy and Pharmaceutical Sciences Binghamton University, Johnson City, NY, 13790, USA.
| | - Katie A Edwards
- Department of Pharmaceutical Sciences School of Pharmacy and Pharmaceutical Sciences Binghamton University, Johnson City, NY, 13790, USA.
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Hinson JS, Rothman RE, Carroll K, Mostafa HH, Ghobadi K, Smith A, Martinez D, Shaw-Saliba K, Klein E, Levin S. Targeted rapid testing for SARS-CoV-2 in the emergency department is associated with large reductions in uninfected patient exposure time. J Hosp Infect 2020; 107:35-39. [PMID: 33038435 PMCID: PMC7538869 DOI: 10.1016/j.jhin.2020.09.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/30/2020] [Accepted: 09/30/2020] [Indexed: 12/05/2022]
Abstract
Opportunity exists to decrease healthcare-related exposure to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), preserve infection control resources, and increase care capacity by reducing the time to diagnosis of coronavirus disease 2019 (COVID-19). A retrospective cohort analysis was undertaken to measure the effect of targeted rapid molecular testing for SARS-CoV-2 on these outcomes. In comparison with standard platform testing, rapid testing was associated with a 65.6% reduction (12.6 h) in the median time to removal from the isolation cohort for patients with negative diagnostic results. This translated to an increase in COVID-19 treatment capacity of 3028 bed-hours and 7500 fewer patient interactions that required the use of personal protective equipment per week.
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Affiliation(s)
- J S Hinson
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - R E Rothman
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - K Carroll
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - H H Mostafa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - K Ghobadi
- Department of Civil and Systems Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD, USA
| | - A Smith
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - D Martinez
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - K Shaw-Saliba
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - E Klein
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S Levin
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Alame D, Hess B, El-Beyrouty C. Antimicrobial Stewardship: What the Clinical Laboratory Needs to Know. Clin Lab Med 2020; 40:509-20. [PMID: 33121619 DOI: 10.1016/j.cll.2020.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Misuse of antibiotics, including unnecessary use or inappropriate selection, may result in side effects and poor outcome in individual patients, as well as contribute to the spread of antimicrobial resistance. Antimicrobial stewardship programs exist to reduce such misuse of antibiotics and ill effect in order to promote patient outcome. The importance of diagnostics, antibiogram data, possible interventions, and impact are reviewed. It is essential for clinical microbiologists and other health care members to understand the field and scope of antimicrobial stewardship, actively participate in, and understand the value they bring to supporting their institution's efforts.
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Mahshid SS, Dabdoub A. Development of a novel electrochemical immuno-biosensor for circulating biomarkers of the inner ear. Biosens Bioelectron 2020; 165:112369. [PMID: 32729501 DOI: 10.1016/j.bios.2020.112369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/23/2022]
Abstract
Current approaches for diagnosis of hearing or vestibular disorders are mostly based on physical examinations that cannot provide information about the exact location of cellular damage inside the inner ear. Therefore, there is a need for new diagnostic methods capable of identifying the sites of damage through the detection of inner ear blood-circulating biomarkers. Here, we developed the first biosensor platform for rapid detection of otolin-1 and prestin, blood-circulating proteins specifically expressed in the vestibule and cochlea, respectively. The platform was designed on a DNA-based immunoassay that employed conjugated antibodies for target protein recognition, which when bound, altered the DNA-DNA hybridization on the surface, resulting in generation of a concentration-dependent signal. The signal was recorded when the redox moiety brought to the surface by the target enabled a selective electrochemical output directly in whole blood. Signal amplification was acquired by employing high-curvature nanostructured electrodes for sensitive sample analysis at picomolar concentrations with a three-fold quantitative range. The combination of nanostructuring and optimum density of the probes on the surface provided low-picomolar detection limits while utilizing small 10 μL sample volume with a 10-min response time. The proposed immuno-biosensor is highly selective and quantitative and can easily be adapted for rapid detection of any blood-circulating protein using their specific antibodies as recognition elements.
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Affiliation(s)
- Sahar S Mahshid
- Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada.
| | - Alain Dabdoub
- Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada; Department of Otolaryngology-Head & Neck Surgery, University of Toronto, Toronto, ON, M5S 3H2, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A1, Canada.
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Briggs N, Campbell S, Gupta S. Advances in rapid diagnostics for bloodstream infections. Diagn Microbiol Infect Dis 2020; 99:115219. [PMID: 33059201 DOI: 10.1016/j.diagmicrobio.2020.115219] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 09/12/2020] [Accepted: 09/12/2020] [Indexed: 10/23/2022]
Abstract
Septicemia from bloodstream infections (BSI) is the second largest cause of inpatient mortality and the single most expensive condition for US hospitals to manage. There has been an explosive development of commercial diagnostic systems to accelerate the identification and antimicrobial susceptibility testing (AST) of causative pathogens. Despite adoption of advanced technologies like matrix-assisted laser desorption imaging-time-of-flight mass spectrometry and multiplex polymerase chain reaction for rapid identification, clinical impact has been variable, in part due to the persistent need for conventional AST as well as prescriber understanding of these rapidly evolving platforms. Newer technologies are expanding on rapid detection of genotypic determinants of resistance, but only recently has rapid phenotypic AST been available. Yet, improved outcomes with rapid diagnostic platforms are still most evident in conjunction with active antimicrobial stewardship. This review will outline key advancements in rapid diagnostics for BSI and the role of antimicrobial stewardship in this new era.
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Affiliation(s)
- Neima Briggs
- Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Sheldon Campbell
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Shaili Gupta
- Department of Medicine, Yale School of Medicine, New Haven, CT; Department of Medicine, Division of Infectious Diseases, VA Healthcare Systems of CT, West Haven, CT.
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Rödel J, Egerer R, Suleyman A, Sommer-Schmid B, Baier M, Henke A, Edel B, Löffler B. Use of the variplex™ SARS-CoV-2 RT-LAMP as a rapid molecular assay to complement RT-PCR for COVID-19 diagnosis. J Clin Virol 2020; 132:104616. [PMID: 32891938 PMCID: PMC7457909 DOI: 10.1016/j.jcv.2020.104616] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 12/23/2022]
Abstract
Rapid detection of SARS-CoV-2 by variplex™ RT-LAMP from respiratory samples. Homogenization of samples using SL solution for testing without RNA elution. Combination of RT-LAMP and RT-PCR increases diagnostic accuracy.
Background Molecular assays based on reverse transcription-loop-mediated isothermal amplification (RT-LAMP) may be useful for rapid diagnosis of the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) because of the easy performance and the option to bypass RNA extraction. Objectives This study was designed to evaluate the clinical performance of the CE-labeled variplexTM real time SARS-CoV-2 RT-LAMP assay in comparison to commercial RT-PCRs. Study design RNA extracted from pharyngeal swabs was tested by variplex™ RT-LAMP and Corman’s LightMix™ E gene RT-PCR as reference. Samples of respiratory secretions from Coronavirus infection disease (COVID-19) and negative control patients were analyzed by variplex™ without RNA extraction and tested in parallel with the Allplex™ and VIASURE BD MAX RT-PCRs. Results Using isolated RNA variplex™ RT-LAMP showed a sensitivity of 75 % compared to LightMix E gene RT-PCR but contrary to the latter it produced no false-positive results. For the evaluation of samples from respiratory secretions concordance analysis showed only a moderate agreement between the variplex™ RT-LAMP conducted on unprocessed samples and Allplex™ and VIASURE RT-PCRs (Cohen’s κ ranging from 0.52−0.56). Using the approach to define a sample as true-positive when at least two assays gave a positive result the clinical sensitivities were as follows: 76.3 % for variplex™, 84.2 % for Allplex™ and 68.4 % for VIASURE. However, when results of RT-PCR and RT-LAMP were combined diagnostic sensitivity was increased to 92–100 %. Conclusion The variplex RT-LAMP may serve as a rapid test to be combined with a RT-PCR assay to increase the diagnostic accuracy in patients with suspected COVID-19 infection.
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Affiliation(s)
- Jürgen Rödel
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany.
| | - Renate Egerer
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | | | | | - Michael Baier
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Andreas Henke
- Section of Experimental Virology, Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Birgit Edel
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, Jena, Germany
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Caméléna F, Moy AC, Dudoignon E, Poncin T, Deniau B, Guillemet L, Le Goff J, Budoo M, Benyamina M, Chaussard M, Coutrot M, Lafaurie M, Plaud B, Mebazaa A, Depret F, Berçot B. Performance of a multiplex polymerase chain reaction panel for identifying bacterial pathogens causing pneumonia in critically ill patients with COVID-19. Diagn Microbiol Infect Dis 2020; 99:115183. [PMID: 33069002 PMCID: PMC7441025 DOI: 10.1016/j.diagmicrobio.2020.115183] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 12/16/2022]
Abstract
The FilmArray® Pneumonia Plus (FA-PP) panel can provide rapid identifications and semiquantitative results for many pathogens. We performed a prospective single-center study in 43 critically ill patients with coronavirus disease 2019 (COVID-19) in which we performed 96 FA-PP tests and cultures of blind bronchoalveolar lavage (BBAL). FA-PP detected 1 or more pathogens in 32% (31/96 of samples), whereas culture methods detected at least 1 pathogen in 35% (34/96 of samples). The most prevalent bacteria detected were Pseudomonas aeruginosa (n = 14) and Staphylococcus aureus (n = 11) on both FA-PP and culture. The FA-PP results from BBAL in critically ill patients with COVID-19 were consistent with bacterial culture findings for bacteria present in the FA-PP panel, showing sensitivity, specificity, and positive and negative predictive value of 95%, 99%, 82%, and 100%, respectively. Median turnaround time for FA-PP was 5.5 h, which was significantly shorter than for standard culture (26 h) and antimicrobial susceptibility testing results (57 h).
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Affiliation(s)
- François Caméléna
- Department of Microbiology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France
| | - Anne-Clotilde Moy
- Department of Anesthesiology and Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Emmanuel Dudoignon
- Department of Anesthesiology and Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 942, INI-CRCT network, Paris, France
| | - Thibaut Poncin
- Department of Microbiology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France
| | - Benjamin Deniau
- Department of Anesthesiology and Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 942, INI-CRCT network, Paris, France
| | - Lucie Guillemet
- Department of Anesthesiology and Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jérôme Le Goff
- Department of Microbiology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Mélissa Budoo
- Department of Microbiology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Mourad Benyamina
- Department of Anesthesiology and Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Maïté Chaussard
- Department of Anesthesiology and Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Maxime Coutrot
- Department of Anesthesiology and Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Matthieu Lafaurie
- Department of Infectious Disease, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Benoît Plaud
- Department of Anesthesiology and Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 942, INI-CRCT network, Paris, France
| | - Alexandre Mebazaa
- Department of Anesthesiology and Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 942, INI-CRCT network, Paris, France
| | - François Depret
- Department of Anesthesiology and Critical Care and Burn Unit, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 942, INI-CRCT network, Paris, France
| | - Béatrice Berçot
- Department of Microbiology, Saint-Louis-Lariboisière Hospital Group, Assistance Publique-Hôpitaux de Paris, Paris, France; University of Paris, INSERM 1137, IAME, Paris, France.
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Stokes W, Pitout J, Campbell L, Church D, Gregson D. Rapid detection of carbapenemase-producing organisms directly from blood cultures positive for Gram-negative bacilli. Eur J Clin Microbiol Infect Dis 2020; 40:381-384. [PMID: 32780248 DOI: 10.1007/s10096-020-04005-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 07/31/2020] [Indexed: 10/23/2022]
Abstract
INTRODUCTION The rapid detection of carbapenemase-producing organisms (CPOs) directly from blood cultures (BCs) positive for Gram-negative bacilli (GNB) may accelerate the appropriate treatment of at-risk patients. OBJECTIVE To evaluate the performance of two commercial assays in the rapid detection of CPOs directly from BC positive for GNB. METHODS BC positive for GNB were tested for the presence of CPOs with β CARBA® and NG-Test® CARBA 5. A subset of sterile BC samples was seeded with multidrug-resistant (MDR) GNB. Positive BCs from clinical and seeded samples were tested directly with β CARBA and CARBA 5 from BC pellets. RESULTS Sixty-five samples were tested (30 clinical, 35 seeded). β CARBA had a sensitivity, specificity, NPV, and PPV of 100%, 65.7%, 100%, and 71.4%, respectively. CARBA 5 had a sensitivity, specificity, NPV, and PPV of 90.0%, 100%, 92.1%, and 100%. False negatives for CARBA 5 occurred with 1 GES, 1 VIM-1, and 1 IMP-14. CONCLUSIONS This study demonstrates that the detection of CPOs directly from positive BC can be accurately achieved. β CARBA had excellent sensitivity but suffered from poor specificity. CARBA 5 had good sensitivity and specificity but is unable to detect certain CPOs.
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Affiliation(s)
- William Stokes
- University of Calgary, Calgary, AB, Canada. .,Alberta Precision Laboratories, Diagnostic & Scientific Centre, 9, 3535 Research Rd NW, Calgary, AB, T2L 2K8, Canada.
| | - Johann Pitout
- University of Calgary, Calgary, AB, Canada.,Alberta Precision Laboratories, Diagnostic & Scientific Centre, 9, 3535 Research Rd NW, Calgary, AB, T2L 2K8, Canada
| | - Lorraine Campbell
- Alberta Precision Laboratories, Diagnostic & Scientific Centre, 9, 3535 Research Rd NW, Calgary, AB, T2L 2K8, Canada
| | - Deirdre Church
- University of Calgary, Calgary, AB, Canada.,Alberta Precision Laboratories, Diagnostic & Scientific Centre, 9, 3535 Research Rd NW, Calgary, AB, T2L 2K8, Canada
| | - Daniel Gregson
- University of Calgary, Calgary, AB, Canada.,Alberta Precision Laboratories, Diagnostic & Scientific Centre, 9, 3535 Research Rd NW, Calgary, AB, T2L 2K8, Canada
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Peiffer-Smadja N, Bouadma L, Mathy V, Allouche K, Patrier J, Reboul M, Montravers P, Timsit JF, Armand-Lefevre L. Performance and impact of a multiplex PCR in ICU patients with ventilator-associated pneumonia or ventilated hospital-acquired pneumonia. Crit Care 2020; 24:366. [PMID: 32560662 PMCID: PMC7303941 DOI: 10.1186/s13054-020-03067-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Early appropriate antibiotic therapy reduces morbidity and mortality of severe pneumonia. However, the emergence of bacterial resistance requires the earliest use of antibiotics with the narrowest possible spectrum. The Unyvero Hospitalized Pneumonia (HPN, Curetis) test is a multiplex PCR (M-PCR) system detecting 21 bacteria and 19 resistance genes on respiratory samples within 5 h. We assessed the performance and the potential impact of the M-PCR on the antibiotic therapy of ICU patients. METHODS In this prospective study, we performed a M-PCR on bronchoalveolar lavage (BAL) or plugged telescoping catheter (PTC) samples of patients with ventilated HAP or VAP with Gram-negative bacilli or clustered Gram-positive cocci. This study was conducted in 3 ICUs in a French academic hospital: the medical and infectious diseases ICU, the surgical ICU, and the cardio-surgical ICU. A multidisciplinary expert panel simulated the antibiotic changes they would have made if the M-PCR results had been available. RESULTS We analyzed 95 clinical samples of ventilated HAP or VAP (72 BAL and 23 PTC) from 85 patients (62 males, median age 64 years). The median turnaround time of the M-PCR was 4.6 h (IQR 4.4-5). A total of 90/112 bacteria were detected by the M-PCR system with a global sensitivity of 80% (95% CI, 73-88%) and specificity of 99% (95% CI 99-100). The sensitivity was better for Gram-negative bacteria (90%) than for Gram-positive cocci (62%) (p = 0.005). Moreover, 5/8 extended-spectrum beta-lactamases (CTX-M gene) and 4/4 carbapenemases genes (3 NDM, one oxa-48) were detected. The M-PCR could have led to the earlier initiation of an effective antibiotic in 20/95 patients (21%) and to early de-escalation in 37 patients (39%) but could also have led to one (1%) inadequate antimicrobial therapy. Among 17 empiric antibiotic treatments with carbapenems, 10 could have been de-escalated in the following hours according to the M-PCR results. The M-PCR also led to 2 unexpected diagnosis of severe legionellosis confirmed by culture methods. CONCLUSIONS Our results suggest that the use of a M-PCR system for respiratory samples of patients with VAP and ventilated HAP could improve empirical antimicrobial therapy and reduce the use of broad-spectrum antibiotics.
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Affiliation(s)
- Nathan Peiffer-Smadja
- Université de Paris, IAME, INSERM, Paris, F-75018, France.
- Infectious and Tropical Diseases Department, Bichat-Claude Bernard Hospital, AP-HP, Paris, 75018, France.
| | - Lila Bouadma
- Université de Paris, IAME, INSERM, Paris, F-75018, France
- Medical and Infectious Diseases ICU (MI2), Bichat-Claude Bernard Hospital, AP-HP, 75018, Paris, France
| | - Vincent Mathy
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Kahina Allouche
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Juliette Patrier
- Medical and Infectious Diseases ICU (MI2), Bichat-Claude Bernard Hospital, AP-HP, 75018, Paris, France
| | - Martin Reboul
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Philippe Montravers
- Département d'Anesthésie Réanimation, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
- INSERM UMR 1152, Physiopathologie et Epidémiologie des Maladies respiratoires, Paris, France
| | - Jean-François Timsit
- Université de Paris, IAME, INSERM, Paris, F-75018, France
- Medical and Infectious Diseases ICU (MI2), Bichat-Claude Bernard Hospital, AP-HP, 75018, Paris, France
| | - Laurence Armand-Lefevre
- Université de Paris, IAME, INSERM, Paris, F-75018, France
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
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Trotter AJ, Dean R, Whitehouse CE, Mikalsen J, Hill C, Brunton-Sim R, Kay GL, Shakokani M, Durst AZE, Wain J, McNamara I, O'Grady J. Preliminary evaluation of a rapid lateral flow calprotectin test for the diagnosis of prosthetic joint infection. Bone Joint Res 2020; 9:202-210. [PMID: 32566141 PMCID: PMC7284294 DOI: 10.1302/2046-3758.95.bjr-2019-0213.r1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Aims This pilot study tested the performance of a rapid assay for diagnosing prosthetic joint infection (PJI), which measures synovial fluid calprotectin from total hip and knee revision patients. Methods A convenience series of 69 synovial fluid samples from revision patients at the Norfolk and Norwich University Hospital were collected intraoperatively (52 hips, 17 knees) and frozen. Synovial fluid calprotectin was measured retrospectively using a new commercially available lateral flow assay for PJI diagnosis (Lyfstone AS) and compared to International Consensus Meeting (ICM) 2018 criteria and clinical case review (ICM-CR) gold standards. Results According to ICM, 24 patients were defined as PJI positive and the remaining 45 were negative. The overall accuracy of the lateral flow test compared to ICM was 75.36% (52/69, 95% CI 63.51% to 84.95%), sensitivity and specificity were 75.00% (18/24, 95% CI 53.29% to 90.23%) and 75.56% (34/45, 95% CI 60.46% to 87.12%), respectively, positive predictive value (PPV) was 62.07% (18/29, 95% CI 48.23% to 74.19%) and negative predictive value (NPV) was 85.00% (34/40, 95% CI 73.54% to 92.04%), and area under the receiver operating characteristic (ROC) curve (AUC) was 0.78 (95% CI 0.66 to 0.87). Patient data from discordant cases were reviewed by the clinical team to develop the ICM-CR gold standard. The lateral flow test performance improved significantly when compared to ICM-CR, with accuracy increasing to 82.61% (57/69, 95% CI 71.59% to 90.68%), sensitivity increasing to 94.74% (18/19, 95% CI 73.97% to 99.87%), NPV increasing to 97.50% (39/40, 95% CI 85.20% to 99.62%), and AUC increasing to 0.91 (95% CI 0.81 to 0.96). Test performance was better in knees (100.00% accurate (17/17, 95% CI 80.49% to 100.00%)) compared to hips (76.92% accurate (40/52, 95% CI 63.16% to 87.47%)). Conclusion This study demonstrates that the calprotectin lateral flow assay could be an effective diagnostic test for PJI, however additional prospective studies testing fresh samples are required. Cite this article:Bone Joint Res. 2020;9(5):202–210.
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Affiliation(s)
- Alexander J Trotter
- University of East Anglia, Norwich, UK, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Rachael Dean
- University of East Anglia, Norwich, UK, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | | | - Claire Hill
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK, Norfolk and Norwich University Hospitals Foundation Trust, Norwich, UK
| | | | - Gemma L Kay
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | - Alexander Z E Durst
- University of East Anglia, Norwich, UK, Norfolk and Norwich University Hospitals Foundation Trust, Norwich, UK
| | - John Wain
- University of East Anglia, Norwich, UK, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Iain McNamara
- University of East Anglia, Norwich, UK, Norfolk and Norwich University Hospitals Foundation Trust, Norwich, UK
| | - Justin O'Grady
- University of East Anglia, Norwich, UK, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
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Steuber TD, Tucker-Heard G, Edwards J, Sawyer A, Thottacherry E, Hassoun A. Utilization and impact of a rapid Candida panel on antifungal stewardship program within a large community hospital. Diagn Microbiol Infect Dis 2020; 97:115086. [PMID: 32535413 DOI: 10.1016/j.diagmicrobio.2020.115086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND The T2 Candida Panel (T2CP) bodes high sensitivity and specificity to detect candidemia, enabling providers to make quick therapy decisions and possibly decrease mortality. However, utilization in practice and clinical application remains to be evaluated. OBJECTIVES To evaluate the overall provider-utilization of the T2CP at a large community hospital. METHODS This single center, retrospective, observational study compared antifungal management in all patients with positive or negative T2CP. Additional endpoints included patient-specific variables influencing antifungal management decisions. RESULTS Six hundred twenty-eight T2CP results were evaluated. Antifungal optimization occurred in 54% of patients who had antifungal orders at the time of T2CP test. Antifungal therapy was avoided in 60.4% of negative cases. Patients with negative T2CP had significantly fewer days of therapy compared to positive tests. CONCLUSIONS Although the T2CP led to fewer days of antifungal therapy with negative tests, many opportunities for improvement in antifungal stewardship were identified, specifically, with negative tests.
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Affiliation(s)
- Taylor D Steuber
- Auburn University Harrison School of Pharmacy, Department of Pharmacy Practice, 301 Governors Drive SW, Huntsville, AL 35801; Huntsville Hospital, Department of Pharmacy, 101 Sivley Road, Huntsville, AL 35801.
| | - Glady's Tucker-Heard
- Auburn University Harrison School of Pharmacy, Department of Pharmacy Practice, 301 Governors Drive SW, Huntsville, AL 35801; Auburn University Harrison School of Pharmacy, Department of Pharmacy Practice, 350 Clinic Drive, Mobile, AL 36688
| | - Jonathan Edwards
- Huntsville Hospital, Department of Pharmacy, 101 Sivley Road, Huntsville, AL 35801
| | - Adam Sawyer
- Huntsville Hospital, Department of Pharmacy, 101 Sivley Road, Huntsville, AL 35801
| | - Elizabeth Thottacherry
- UAB Huntsville Regional Medical Campus, Department of Internal Medicine, 301 Governors Drive SW, Huntsville, AL 35801
| | - Ali Hassoun
- Alabama Infectious Diseases Center, 420 Lowell Dr SE #301, Huntsville, AL
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Pillai SP, Prentice KW, Ramage JG, DePalma L, Sarwar J, Parameswaran N, Bell M, Plummer A, Santos A, Singh A, Pillai CA, Thirunavvukarasu N, Manickam G, Avila JR, Sharma SK, Hoffmaster A, Anderson K, Morse SA, Venkateswaran KV, Hodge DR. Rapid Presumptive Identification of Bacillus anthracis Isolates Using the Tetracore RedLine Alert™ Test. Health Secur 2020; 17:334-343. [PMID: 31433282 DOI: 10.1089/hs.2019.0038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A comprehensive laboratory evaluation of the Tetracore RedLine Alert test, a lateral flow immunoassay (LFA) for the rapid presumptive identification of Bacillus anthracis, was conducted at 2 different test sites. The study evaluated the sensitivity of this assay using 16 diverse strains of B. anthracis grown on sheep blood agar (SBA) plates. In addition, 83 clinically relevant microorganisms were tested to assess the specificity of the RedLine Alert test. The results indicated that the RedLine Alert test for the presumptive identification of B. anthracis is highly robust, specific, and sensitive. RedLine Alert is a rapid test that has applicability for use in a clinical setting for ruling-in or ruling-out nonhemolytic colonies of Bacillus spp. grown on SBA medium as presumptive isolates of B. anthracis.
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Affiliation(s)
- Segaran P Pillai
- Segaran P. Pillai, PhD, is Director, Office of Laboratory Science and Safety, FDA Office of the Commissioner, Department of Health and Human Services, Silver Spring, MD
| | - Kristin W Prentice
- Kristin W. Prentice, MS, is an Associate, and Lindsay DePalma, MS, is a Staff Life Scientist; both at Booz Allen Hamilton, Rockville, MD
| | - Jason G Ramage
- Jason G. Ramage, MS, MBA, PMP, is Assistant Vice Chancellor for Research and Innovation and Director of Research Compliance, University of Arkansas, Fayetteville, AR
| | - Lindsay DePalma
- Kristin W. Prentice, MS, is an Associate, and Lindsay DePalma, MS, is a Staff Life Scientist; both at Booz Allen Hamilton, Rockville, MD
| | - Jawad Sarwar
- Jawad Sarwar, MS, is a Senior Research Scientist, and Nishanth Parameswaran is a Research Scientist; both at Omni Array Biotechnology, Rockville, MD
| | - Nishanth Parameswaran
- Jawad Sarwar, MS, is a Senior Research Scientist, and Nishanth Parameswaran is a Research Scientist; both at Omni Array Biotechnology, Rockville, MD
| | - Melissa Bell
- Melissa Bell, MS, is a Microbiologist, and Alex Hoffmaster, PhD, is Chief, Bacterial Special Pathogens Branch; both in the National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Andrea Plummer
- Andrea Plummer and Alan Santos are Microbiologists, and Kodumudi Venkat Venkateswaran, PhD, is Chief Scientist; all at Tetracore, Inc., Rockville, MD
| | - Alan Santos
- Andrea Plummer and Alan Santos are Microbiologists, and Kodumudi Venkat Venkateswaran, PhD, is Chief Scientist; all at Tetracore, Inc., Rockville, MD
| | - Ajay Singh
- Ajay Singh, PhD, is a Research Scientist, Laulima Government Solutions, Contractor Support to USAMRICD Neurobiological Toxicology Branch, Analytical Toxicology Division, Aberdeen Proving Ground, MD
| | - Christine A Pillai
- Christine A. Pillai, Nagarajan Thirunavvukarasu, PhD, and Gowri Manickam, PhD, are ORISE Fellow Research Scientists, and Shashi K. Sharma, PhD, is a Research Microbiologist; all with the FDA Center for Food Safety and Applied Nutrition, Molecular Methods Development Branch, Division of Microbiology, Office of Regulatory Science, College Park, MD
| | - Nagarajan Thirunavvukarasu
- Christine A. Pillai, Nagarajan Thirunavvukarasu, PhD, and Gowri Manickam, PhD, are ORISE Fellow Research Scientists, and Shashi K. Sharma, PhD, is a Research Microbiologist; all with the FDA Center for Food Safety and Applied Nutrition, Molecular Methods Development Branch, Division of Microbiology, Office of Regulatory Science, College Park, MD
| | - Gowri Manickam
- Christine A. Pillai, Nagarajan Thirunavvukarasu, PhD, and Gowri Manickam, PhD, are ORISE Fellow Research Scientists, and Shashi K. Sharma, PhD, is a Research Microbiologist; all with the FDA Center for Food Safety and Applied Nutrition, Molecular Methods Development Branch, Division of Microbiology, Office of Regulatory Science, College Park, MD
| | - Julie R Avila
- Julie R. Avila, MS, is a Scientific Associate, Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA
| | - Shashi K Sharma
- Christine A. Pillai, Nagarajan Thirunavvukarasu, PhD, and Gowri Manickam, PhD, are ORISE Fellow Research Scientists, and Shashi K. Sharma, PhD, is a Research Microbiologist; all with the FDA Center for Food Safety and Applied Nutrition, Molecular Methods Development Branch, Division of Microbiology, Office of Regulatory Science, College Park, MD
| | - Alex Hoffmaster
- Melissa Bell, MS, is a Microbiologist, and Alex Hoffmaster, PhD, is Chief, Bacterial Special Pathogens Branch; both in the National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Kevin Anderson
- Kevin Anderson, PhD, and David R. Hodge, PhD, are Program Managers, Science and Technology Directorate, US Department of Homeland Security, Washington, DC
| | - Stephen A Morse
- Stephen A. Morse, MSPH, PhD, is a Senior Advisor, CDC Division of Select Agents and Toxins, and is currently with IHRC, Inc., Atlanta, GA
| | - Kodumudi Venkat Venkateswaran
- Andrea Plummer and Alan Santos are Microbiologists, and Kodumudi Venkat Venkateswaran, PhD, is Chief Scientist; all at Tetracore, Inc., Rockville, MD
| | - David R Hodge
- Kevin Anderson, PhD, and David R. Hodge, PhD, are Program Managers, Science and Technology Directorate, US Department of Homeland Security, Washington, DC
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Lenhard JR, Rana AP, Wenzler E, Huang Y, Kreiswirth BN, Chen L, Bulman ZP. A coup d'état by NDM-producing Klebsiella pneumoniae overthrows the major bacterial population during KPC-directed therapy. Diagn Microbiol Infect Dis 2020; 98:115080. [PMID: 32619895 DOI: 10.1016/j.diagmicrobio.2020.115080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/17/2020] [Accepted: 05/08/2020] [Indexed: 10/24/2022]
Abstract
The objective of this study was to utilize a co-culture hollow-fiber infection model (HFIM) to characterize the interplay between a small, difficult-to-detect, New Delhi metallo-β-lactamase-producing Klebsiella pneumoniae (NDM-Kp) minor population and a larger K. pneumoniae carbapenemase (KPC)-producing K. pneumoniae population in the presence of KPC-directed antibacterial therapy. Selective plating onto agar with ceftazidime-avibactam was used to track the density of the NDM-Kp population. Susceptibility testing and the Verigene System failed to identify the small initial NDM-Kp population. However, a ceftazidime-avibactam Etest detected resistant colonies that were confirmed to be NDM-Kp. In the HFIM, all of the investigated drug regimens caused regrowth within 24 h and resulted in >109 CFU/mL of NDM-Kp. Our study demonstrates that the HFIM is a powerful tool for studying the population dynamics of multiple pathogens during antimicrobial exposure and also highlights that difficult-to-detect minor populations of drug-resistant bacteria may cause treatment failure without appropriate antibacterial therapy.
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Affiliation(s)
- Justin R Lenhard
- California Northstate University College of Pharmacy, Elk Grove, CA, USA
| | - Amisha P Rana
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Eric Wenzler
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Yanqin Huang
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Zackery P Bulman
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA.
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Poole S, Clark TW. Rapid syndromic molecular testing in pneumonia: The current landscape and future potential. J Infect 2020; 80:1-7. [PMID: 31809764 PMCID: PMC7132381 DOI: 10.1016/j.jinf.2019.11.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 12/18/2022]
Abstract
Community acquired pneumonia (CAP), hospital-acquired pneumonia (HAP) and ventilator associated pneumonia (VAP) are all associated with significant mortality and cause huge expense to health care services around the world. Early, appropriate antimicrobial therapy is crucial for effective treatment. Syndromic diagnostic testing using novel, rapid multiplexed molecular platforms represents a new opportunity for rapidly targeted antimicrobial therapy to improve patient outcomes and facilitate antibiotic stewardship. In this article we review the currently available testing platforms and discuss the potential benefits and pitfalls of rapid testing in pneumonia.
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Affiliation(s)
- Stephen Poole
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust Southampton, United Kingdom.
| | - Tristan W Clark
- School of Clinical and Experimental Sciences, University of Southampton and NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
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Voermans JJC, Mulders DGJC, Pas SD, Koopmans MPG, van der Eijk AA, Molenkamp R. Performance evaluation of the Panther Fusion® respiratory tract panel. J Clin Virol 2020; 123:104232. [PMID: 31869661 DOI: 10.1016/j.jcv.2019.104232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/29/2019] [Accepted: 12/09/2019] [Indexed: 12/21/2022]
Abstract
Clinical specificity of Panther Fusion® is between 96 %–100 %, compared to LDT. Clinical sensitivity Panther Fusion® is between 71.9 %–100 %, compared to LDT. Overall linear regression showed good correlations between LDT and Panther Fusion® for all viruses, except RV and PIV-4. The Panther Fusion® provides a random-access system with continuous loading and shorter sample-to-answer times compared to LDT.
Background Respiratory tract infections are among the most common infections during winter season. Rapid diagnostics is required for clinical decision making regarding isolation of patients and appropriate therapy. Objectives The aim of this study was to evaluate the analytical and clinical performance characteristics of the Panther Fusion® respiratory panel using published laboratory-developed real-time PCR assays (LDT). Study design Analytical sensitivity of Panther Fusion® Flu A/B/RSV was assessed by testing dilutions of cell culture isolates. Clinical performance assessment included the complete Panther Fusion® respiratory panel (Flu-A/B/RSV, PIV 1-4 and AdV/hMPV/RV) and consisted of a retrospective and a prospective study-arm. The retrospective evaluation included 201, stored (−80 °C) samples collected between February 2006 and January 2017. Prospective evaluation was performed on 1045 unselected pretreated respiratory tract samples from patients presented to our hospital between November 2017 and May 2018. Results Analytical sensitivity was generally slightly lower for the Panther Fusion® assays. Clinical specificity and sensitivity was between 96 %–100 % and 71.9 %–100 %, respectively. Discrepant results were found in 146 samples of which 88 samples tested LDT positive / Panther Fusion® negative and 58 samples were LDT negative / Panther Fusion® positive. A total of ten discrepant samples with Ct-values <30 were sequenced to confirm the presence of 7 RV-C not-detected by LDT and 1 RV-A and 2 ADV-2 not detected by Panther Fusion®. Conclusions The Panther Fusion® provides a random-access system with continuous loading and much shorter sample-to-answer times compared to LDT, albeit with a slightly less clinical sensitivity compared to the LDT.
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Chavada R, Clifford L, Weisback O. Clinical impact of rapid diagnostics using Xpert Flu/RSV™ PCR on antimicrobial stewardship initiatives during influenza season. Infect Dis Health 2019; 25:71-76. [PMID: 31813791 DOI: 10.1016/j.idh.2019.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 11/17/2022]
Abstract
BACKGROUND Despite the availability of several rapid Influenza tests (RIT), the literature on its impact on antimicrobial stewardship programs (AMS) is minimal. Studies utilising rapid point of care tests (POCT) have shown benefit in terms of shortening antimicrobial therapy and prescriptions of antivirals. We designed this study to assess whether RIT had an impact on antibiotic cessation. METHODS Xpert Flu/RSV (Cepheid, CA) was performed on all patients who presented with influenza-like illness (ILI) in 2017. Clinical data was collected from electronic medical records (eMR). Patients with RSV were not included. Turnaround time (TAT) for the test was time from specimen collection until when the result was either notified or appeared on eMR. Standard univariate analysis and multivariable regression analysis (MVRA) were done. RESULTS A total of 665 patients tested positive-Influenza A (63%) and B (37%). After positive results, antimicrobials were ceased in 34% (226/665) or not given in 10% (71/665) cases. Median TAT was 7 h, with 50% of tests completed in less than 6 h 56% (368/665) of patients had their antibiotics continued. On MVRA, results of RIT within 6-12 h resulted in most antibiotic cessation (73%, OR 1.55, p = 0.01). It was found that antibiotics are continued in immunosuppressed patients (OR 2.88, p < 0.01), patients with pneumonia (OR 18.8, p < 0.01) and with underlying COPD (OR 2.43, p = 0.03). CONCLUSION Influenza patients are more likely to have their antibiotics continued with underlying COPD, pneumonia, or immunosuppression. Results of RIT within 6-12 h can help clinicians in deciding on cessation of antibiotics in patients.
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Affiliation(s)
| | - Liam Clifford
- Department of Medicine, Gosford/Wyong Hospital, Gosford, NSW, 2250, Australia
| | - Owen Weisback
- Department of Medicine, Gosford/Wyong Hospital, Gosford, NSW, 2250, Australia
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50
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Butler DA, Biagi M, Tan X, Qasmieh S, Bulman ZP, Wenzler E. Multidrug Resistant Acinetobacter baumannii: Resistance by Any Other Name Would Still be Hard to Treat. Curr Infect Dis Rep 2019; 21:46. [PMID: 31734740 DOI: 10.1007/s11908-019-0706-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW Acinetobacter baumannii (AB) is an infamous nosocomial pathogen with a seemingly limitless capacity for antimicrobial resistance, leading to few treatment options and poor clinical outcomes. The debatably low pathogenicity and virulence of AB are juxtaposed by its exceptionally high rate of infection-related mortality, likely due to delays in time to effective antimicrobial therapy secondary to its predilection for resistance to first-line agents. Recent studies of AB and its infections have led to a burgeoning understanding of this critical microbial threat and provided clinicians with new ammunition for which to target this elusive pathogen. This review will provide an update on the virulence, resistance, diagnosis, and treatment of multidrug resistant (MDR) AB. RECENT FINDINGS Advances in bacterial genomics have led to a deeper understanding of the unique mechanisms of resistance often present in MDR AB and how they may be exploited by new antimicrobials or optimized combinations of existing agents. Further, improvements in rapid diagnostic tests (RDTs) and their more pervasive use in combination with antimicrobial stewardship interventions have allowed for more rapid diagnosis of AB and decreases in time to effective therapy. Unfortunately, there remains a paucity of high-quality clinical data for which to inform the optimal treatment of MDR AB infections. In fact, recently completed studies have failed to identify a combination regimen that is consistently superior to monotherapy, despite the benefits demonstrated in vitro. Encouragingly, new and updated guidelines offer strategies for the treatment of MDR AB and may help to harmonize the use of high toxicity agents such as the polymyxins. Finally, new antimicrobial agents such as eravacycline and cefiderocol have promising in vitro activity against MDR AB but their place in therapy for these infections remains to be determined. Notwithstanding available clinical trial data, polymyxin-based combination therapies with either a carbapenem, minocycline, or eravacycline remain the treatment of choice for MDR, particularly carbapenem-resistant, AB. Incorporating antimicrobial stewardship intervention with RDTs relevant to MDR AB can help avoid potentially toxic combination therapies and catalyze the most important modifiable risk factor for mortality-time to effective therapy. Further research efforts into pharmacokinetic/pharmacodynamic-based dose optimization and clinical outcomes data for MDR AB continue to be desperately needed.
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Affiliation(s)
- David A Butler
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Room 164 (M/C 886), Chicago, IL, 60612, USA
| | - Mark Biagi
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Room 164 (M/C 886), Chicago, IL, 60612, USA
| | - Xing Tan
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Room 164 (M/C 886), Chicago, IL, 60612, USA
| | - Samah Qasmieh
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Room 164 (M/C 886), Chicago, IL, 60612, USA
| | - Zackery P Bulman
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Room 164 (M/C 886), Chicago, IL, 60612, USA
| | - Eric Wenzler
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, 833 South Wood Street, Room 164 (M/C 886), Chicago, IL, 60612, USA.
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