1
|
Dessajan J, Timsit JF. Impact of Multiplex PCR in the Therapeutic Management of Severe Bacterial Pneumonia. Antibiotics (Basel) 2024; 13:95. [PMID: 38247654 PMCID: PMC10812737 DOI: 10.3390/antibiotics13010095] [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: 12/26/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024] Open
Abstract
Pneumonia is a common and severe illness that requires prompt and effective management. Advanced, rapid, and accurate tools are needed to diagnose patients with severe bacterial pneumonia, and to rapidly select appropriate antimicrobial therapy, which must be initiated within the first few hours of care. Two multiplex molecular tests, Unyvero HPN and FilmArray Pneumonia+ Panel, have been developed using the multiplex polymerase chain reaction (mPCR) technique to rapidly identify pathogens and their main antibiotic resistance mechanisms from patient respiratory specimens. Performance evaluation of these tests showed strong correlations with reference techniques. However, good knowledge of their indications, targets, and limitations is essential. Collaboration with microbiologists is, therefore, crucial for their appropriate use. Under these conditions, and with standardized management, these rapid tests can improve the therapeutic management of severe pneumonia faster, more precisely, and with narrow-spectrum antibiotic therapy. Further randomized controlled trials are needed to address the many unanswered questions about multiplex rapid molecular testing during the diagnosis and the management of severe pneumonia. This narrative review will address the current knowledge, advantages, and disadvantages of these tests, and propose solutions for their routine use.
Collapse
Affiliation(s)
- Julien Dessajan
- Assistance Publique Hôpitaux de Paris (AP-HP), Medical and Infectious Diseases Intensive Care Unit, Bichat Claude-Bernard Hospital, Paris Cité University, 46 Rue Henri Huchard, 75018 Paris, France;
| | - Jean-François Timsit
- Assistance Publique Hôpitaux de Paris (AP-HP), Medical and Infectious Diseases Intensive Care Unit, Bichat Claude-Bernard Hospital, Paris Cité University, 46 Rue Henri Huchard, 75018 Paris, France;
- Mixt Research Unit (UMR) 1137, Infection, Antimicrobials, Modelization, Epidemiology (IAME), Institut National de la Recherche Médicale (INSERM), Paris Cité University, 75018 Paris, France
| |
Collapse
|
2
|
Wettengel JM, Strehle K, von Lucke C, Roggendorf H, Jeske SD, Christa C, Zelger O, Haller B, Protzer U, Knolle PA. Improved detection of infection with SARS-CoV-2 Omicron variants of concern in healthcare workers by a second-generation rapid antigen test. Microbiol Spectr 2023; 11:e0176823. [PMID: 37831440 PMCID: PMC10714798 DOI: 10.1128/spectrum.01768-23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE The results from this study demonstrate the usefulness of a second-generation rapid antigen test for early detection of infection with the SARS-CoV-2 Omicron variant of concern (VoC) and reveal a higher sensitivity to detect immune escape Omicron VoCs compared to a first-generation rapid antigen test (89.4% vs 83.7%) in the high-risk group of healthcare workers.
Collapse
Affiliation(s)
- Jochen M. Wettengel
- Institute of Virology, School of Medicine and Health, Technical University of Munich (TUM), München, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, München, Germany
| | - Katharina Strehle
- Institute of Molecular Immunology, School of Medicine and Health, TUM, München, Germany
- Coronavirus Diagnostic Center of the University Hospital München Rechts der Isar, School of Medicine, TUM, München, Germany
| | - Catharina von Lucke
- Coronavirus Diagnostic Center of the University Hospital München Rechts der Isar, School of Medicine, TUM, München, Germany
| | - Hedwig Roggendorf
- Institute of Molecular Immunology, School of Medicine and Health, TUM, München, Germany
- Coronavirus Diagnostic Center of the University Hospital München Rechts der Isar, School of Medicine, TUM, München, Germany
| | - Samuel D. Jeske
- Institute of Virology, School of Medicine and Health, Technical University of Munich (TUM), München, Germany
| | - Catharina Christa
- Institute of Virology, School of Medicine and Health, Technical University of Munich (TUM), München, Germany
| | - Otto Zelger
- Coronavirus Diagnostic Center of the University Hospital München Rechts der Isar, School of Medicine, TUM, München, Germany
| | - Bernhard Haller
- Institute for AI and Informatics in Medicine Statistics, School of Medicine and Health, TUM, München, Germany
| | - Ulrike Protzer
- Institute of Virology, School of Medicine and Health, Technical University of Munich (TUM), München, Germany
- German Center for Infection Research (DZIF), Munich Partner Site, München, Germany
- Institute of Virology, Helmholtz Munich, München, Germany
| | - Percy A. Knolle
- German Center for Infection Research (DZIF), Munich Partner Site, München, Germany
- Institute of Molecular Immunology, School of Medicine and Health, TUM, München, Germany
| |
Collapse
|
3
|
Giacobbe DR, Di Pilato V, Karaiskos I, Giani T, Marchese A, Rossolini GM, Bassetti M. Treatment and diagnosis of severe KPC-producing Klebsiella pneumoniae infections: a perspective on what has changed over last decades. Ann Med 2023; 55:101-113. [PMID: 36856521 PMCID: PMC9980017 DOI: 10.1080/07853890.2022.2152484] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Antimicrobial resistance is a global health threat. Among Gram-negative bacteria, resistance to carbapenems, a class of β-lactam antibiotics, is usually a proxy for difficult-to-treat resistance, since carbapenem-resistant organisms are often resistant to many classes of antibiotics. Carbapenem resistance in the Gram-negative pathogen Klebsiella pneumoniae is mostly due to the production of carbapenemases, enzymes able to hydrolyze carbapenems, and K. pneumoniae carbapenemase (KPC)-type enzymes are overall the most prevalent carbapenemases in K. pneumoniae. In the last decade, the management of severe infections due to KPC-producing K. pneumoniae (KPC-Kp) in humans has presented many peculiar challenges to clinicians worldwide. In this perspective, we discuss how the treatment of severe KPC-Kp infections has evolved over the last decades, guided by the accumulating evidence from clinical studies, and how recent advances in diagnostics have allowed to anticipate identification of KPC-Kp in infected patients.KEY MESSAGESIn the last decade, the management of severe infections due to KPC-Kp has presented many peculiar challenges to clinicians worldwideFollowing the introduction in clinical practice of novel β-lactam/β-lactamase inhibitor combinations and novel β-lactams active against KPC-producing bacteria, the management of severe KPC-Kp infections has witnessed a remarkable evolutionTreatment of severe KPC-Kp infections is a highly dynamic process, in which the wise use of novel antimicrobials should be accompanied by a continuous refinement based on evolving clinical evidence and laboratory diagnostics.
Collapse
Affiliation(s)
- Daniele Roberto Giacobbe
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy.,UO Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - Ilias Karaiskos
- First Department of Internal Medicine - Infectious Diseases, Hygeia General Hospital, Athens, Greece
| | - Tommaso Giani
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Anna Marchese
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy.,UO Microbiologia, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Clinical Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Matteo Bassetti
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy.,UO Clinica Malattie Infettive, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| |
Collapse
|
4
|
Calderon-Ruiz P, Haist G, Mascus A, Holguin-Rocha AF, Koliopoulos P, Daniel T, Velez G, Londono-Renteria B, Gröndahl B, Tobon-Castano A, Gehring S. Multiplex Reverse Transcription Polymerase Chain Reaction Combined with a Microwell Hybridization Assay Screening for Arbovirus and Parasitic Infections in Febrile Patients Living in Endemic Regions of Colombia. Trop Med Infect Dis 2023; 8:466. [PMID: 37888594 PMCID: PMC10610613 DOI: 10.3390/tropicalmed8100466] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 09/29/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
Acute febrile syndrome is a frequent reason for medical consultations in tropical and subtropical countries where the cause could have an infectious origin. Malaria and dengue are the primary etiologies in Colombia. As such, constant epidemiological surveillance and new diagnostic tools are required to identify the causative agents. A descriptive cross-sectional study was conducted to evaluate the circulation and differential diagnosis of six pathogens in two regions of Colombia. The results obtained via multiplex reverse transcription polymerase chain reaction combined with a microwell hybridization assay (m-RT-PCR-ELISA) were comparable to those obtained using rapid tests conducted at the time of patient enrollment. Of 155 patients evaluated, 25 (16.1%) and 16 (10.3%) were positive for malaria and dengue, respectively; no samples were positive for any of the other infectious agents tested. In most cases, m-RT-PCR-ELISA confirmed the results previously obtained through rapid testing.
Collapse
Affiliation(s)
- Paula Calderon-Ruiz
- Center of Pediatric and Adolescent Medicine, University Medical Center, 55131 Mainz, Germany; (G.H.); (A.M.); (P.K.); (T.D.); (B.G.); (S.G.)
- Malaria Group, Lab 610, Faculty of Medicine, University of Antioquia, Medellin 050010, Colombia; (G.V.); (A.T.-C.)
| | - Gregor Haist
- Center of Pediatric and Adolescent Medicine, University Medical Center, 55131 Mainz, Germany; (G.H.); (A.M.); (P.K.); (T.D.); (B.G.); (S.G.)
| | - Annina Mascus
- Center of Pediatric and Adolescent Medicine, University Medical Center, 55131 Mainz, Germany; (G.H.); (A.M.); (P.K.); (T.D.); (B.G.); (S.G.)
| | - Andres F. Holguin-Rocha
- Department of Entomology, College of Agriculture, Kansas State University, Manhattan, KS 66506, USA;
| | - Philip Koliopoulos
- Center of Pediatric and Adolescent Medicine, University Medical Center, 55131 Mainz, Germany; (G.H.); (A.M.); (P.K.); (T.D.); (B.G.); (S.G.)
| | - Tim Daniel
- Center of Pediatric and Adolescent Medicine, University Medical Center, 55131 Mainz, Germany; (G.H.); (A.M.); (P.K.); (T.D.); (B.G.); (S.G.)
| | - Gabriel Velez
- Malaria Group, Lab 610, Faculty of Medicine, University of Antioquia, Medellin 050010, Colombia; (G.V.); (A.T.-C.)
| | - Berlin Londono-Renteria
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA;
| | - Britta Gröndahl
- Center of Pediatric and Adolescent Medicine, University Medical Center, 55131 Mainz, Germany; (G.H.); (A.M.); (P.K.); (T.D.); (B.G.); (S.G.)
| | - Alberto Tobon-Castano
- Malaria Group, Lab 610, Faculty of Medicine, University of Antioquia, Medellin 050010, Colombia; (G.V.); (A.T.-C.)
| | - Stephan Gehring
- Center of Pediatric and Adolescent Medicine, University Medical Center, 55131 Mainz, Germany; (G.H.); (A.M.); (P.K.); (T.D.); (B.G.); (S.G.)
| |
Collapse
|
5
|
Markussen DL, Ebbesen M, Serigstad S, Knoop ST, Ritz C, Bjørneklett R, Kommedal Ø, Jenum S, Ulvestad E, Grewal HMS. The diagnostic utility of microscopic quality assessment of sputum samples in the era of rapid syndromic PCR testing. Microbiol Spectr 2023; 11:e0300223. [PMID: 37772853 PMCID: PMC10581175 DOI: 10.1128/spectrum.03002-23] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 08/11/2023] [Indexed: 09/30/2023] Open
Abstract
This prospective study assessed the value of initial microscopy evaluation of sputum samples submitted for rapid syndromic PCR-based testing. Bacterial detections by the BioFire FilmArray Pneumonia Panel plus in 126 high- and 108 low-quality sputum samples, based on initial microscopy evaluation in samples from patients with lower respiratory tract infections were compared. We found that high-quality samples had a higher proportion of bacterial detections compared to low-quality samples (P = 0.013). This included a higher proportion of detections of bacteria deemed clinically relevant by predefined criteria (70% and 55%, P = 0.016), as well as a higher proportion of detections of Haemophilus influenzae (36% and 20%, P = 0.010). High-quality samples also had more detections of bacteria with high semi-quantitative values. The study found no significant difference between high- and low-quality samples in the proportions of samples with a single species of bacteria detected, samples with a bacteria treated by the clinician, samples with detection of a proven etiology of community-acquired pneumonia by predefined criteria, the number of bacterial species detected, or the detection of Streptococcus pneumoniae, Moraxella catarrhalis, or Staphylococcus aureus. The results showed that 40% (95% CI 35%-47%) of the bacterial detections would have been missed if only high-quality samples were analyzed. This included 41% (27%-56%) of detections of S. pneumoniae, 33% (23%-45%) of detections of H. influenzae, 42% (28%-58%) of detections of S. aureus, and 37% (23%-54%) of detections of M. catarrhalis. These findings suggest that all sputum samples submitted for rapid syndromic PCR testing should be analyzed, regardless of initial microscopy quality assessment. (This study has been registered at ClinicalTrials.gov under registration no. NCT04660084.) IMPORTANCE Microscopic quality assessment of sputum samples was originally designed for sputum culture, and its applicability in today's workflow, which includes syndromic PCR testing, may differ. Addressing this crucial gap, our study emphasizes the need to optimize the use and workflow of syndromic PCR panels, like the BioFire FilmArray Pneumonia plus (FAP plus), in microbiology laboratories. These advanced PCR-based tests offer rapid and comprehensive pathogen detection for respiratory infections, yet their full potential remains uncertain. By comparing bacterial detections in high- and low-quality sputum samples, we underscore the importance of including low-quality samples in testing. Our findings reveal a significant proportion of potentially clinically relevant bacterial detections that would have been missed if only high-quality samples were analyzed. These insights support the efficient implementation of syndromic PCR panels, ultimately enhancing patient care and outcomes.
Collapse
Affiliation(s)
- Dagfinn Lunde Markussen
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Marit Ebbesen
- Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Sondre Serigstad
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, 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
| | - Rune Bjørneklett
- Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Medicine, Faculty of Medicine, University of Bergen, 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
| | - Synne Jenum
- Department of Clinical Science, Bergen Integrated Diagnostic Stewardship Cluster, Faculty of Medicine, University of Bergen, Bergen, Norway
- Department of Infectious Diseases, Oslo University Hospital, Oslo, 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
| |
Collapse
|
6
|
Santos HO, Santos EMS, de Oliveira HDS, dos Santos WS, Tupy AA, Souza EG, Ramires R, Luiz ACO, de Almeida AC. Screening for canine coronavirus, canine influenza virus, and severe acute respiratory syndrome coronavirus 2 in dogs during the coronavirus disease-2019 pandemic. Vet World 2023; 16:1772-1780. [PMID: 37859971 PMCID: PMC10583864 DOI: 10.14202/vetworld.2023.1772-1780] [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: 03/13/2023] [Accepted: 07/26/2023] [Indexed: 10/21/2023] Open
Abstract
Background and Aim Although most cases of coronavirus disease-2019 (COVID-19) are in humans, there is scientific evidence to suggest that the virus can also infect dogs and cats. This study investigated the circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), canine coronavirus (CCV), and canine influenza virus (CIV) in domiciled and/or stray dogs from different locations in the State of Minas Gerais, Brazil, during the COVID-19 pandemic. Materials and Methods In total, 86 dogs living in homes, on the streets, or in shelters in the cities of Taiobeiras, Salinas, Araçuaí, and Almenara were randomly selected for this study. The COVID Ag Detect® Self-Test was used to detect SARS-CoV-2. The ACCUVET CCV AG TEST - CANINE CORONAVIROSIS® was used to detect CCV, whereas canine influenza was detected using the ACCUVET CIV AG TEST - INFLUENZA CANINA®. All collected data were mapped using QGIS 3.28.1 for spatial data analysis and the identification of disease distribution patterns. Descriptive analysis of the collected data, prevalence calculations, odds ratios (ORs), and 95% confidence intervals, when possible, was performed. Results Of the 86 animals tested, only one dog tested positive for SARS-CoV-2 using the rapid test for viral antigen detection. No animals tested positive for CIV. Canine coronavirus was detected in almost half of the animals tested in Almenara. Severe acute respiratory syndrome-CoV-2 had a low prevalence (1.16%), versus 15.62% for CCV. Although the results were not significant, the age and breed of animals appeared to be associated with the occurrence of CCV. The results indicated that younger animals were 2.375-fold more likely to be infected. Likewise, purebred animals were more likely to contract the disease (OR = 1.944). Conclusion The results indicate the need to maintain preventive measures against CCV, canine influenza, and SARS-CoV-2 in dogs. More studies are needed to better elucidate the panorama of these diseases in dogs, mainly in underdeveloped and developing countries.
Collapse
Affiliation(s)
| | | | | | | | | | - Elber Gomes Souza
- Clínica Veterinária e Pet Shop Neres e Souza, Salinas, Minas Gerais, Brazil
| | - Rair Ramires
- Zecão pet shop clínica veterinária, Salinas, Minas Gerais, Brazil
| | | | - Anna Christina de Almeida
- Institute of Agricultural Sciences, Federal University of Minas Gerais, Montes Claros, Minas Gerais, Brazil
| |
Collapse
|
7
|
Major SR, Harke MJ, Cruz-Flores R, Dhar AK, Bodnar AG, Wanamaker SA. Rapid Detection of DNA and RNA Shrimp Viruses Using CRISPR-Based Diagnostics. Appl Environ Microbiol 2023:e0215122. [PMID: 37219435 DOI: 10.1128/aem.02151-22] [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] [Indexed: 05/24/2023] Open
Abstract
Timely detection of persistent and emerging pathogens is critical to controlling disease spread, particularly in high-density populations with increased contact between individuals and limited-to-no ability to quarantine. Standard molecular diagnostic tests for surveying pathogenic microbes have provided the sensitivity needed for early detection, but lag in time-to-result leading to delayed action. On-site diagnostics alleviate this lag, but current technologies are less sensitive and adaptable than lab-based molecular methods. Towards the development of improved on-site diagnostics, we demonstrated the adaptability of a loop-mediated isothermal amplification-CRISPR coupled technology for detecting DNA and RNA viruses that have greatly impacted shrimp populations worldwide; White Spot Syndrome Virus and Taura Syndrome Virus. Both CRISPR-based fluorescent assays we developed showed similar sensitivity and accuracy for viral detection and load quantification to real-time PCR. Additionally, both assays specifically targeted their respective virus with no false positives detected in animals infected with other common pathogens or in certified specific pathogen-free animals. IMPORTANCE The Pacific white shrimp (Penaeus vannamei) is one of the most valuable aquaculture species in the world but has suffered major economic losses from outbreaks of White Spot Syndrome Virus and Taura Syndrome Virus. Rapid detection of these viruses can improve aquaculture practices by enabling more timely action to be taken to combat disease outbreaks. Highly sensitive, specific, and robust CRISPR-based diagnostic assays such as those developed here have the potential to revolutionize disease management in agriculture and aquaculture helping to promote global food security.
Collapse
Affiliation(s)
- Samuel R Major
- Gloucester Marine Genomics Institute, Gloucester, Massachusetts, USA
| | - Matthew J Harke
- Gloucester Marine Genomics Institute, Gloucester, Massachusetts, USA
| | - Roberto Cruz-Flores
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Arun K Dhar
- Aquaculture Pathology Laboratory, School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Andrea G Bodnar
- Gloucester Marine Genomics Institute, Gloucester, Massachusetts, USA
| | | |
Collapse
|
8
|
Ekwall-Larson A, Fröding I, Mert B, Åkerlund A, Özenci V. Analytical Performance and Potential Clinical Utility of EUCAST Rapid Antimicrobial Susceptibility Testing in Blood Cultures after Four Hours of Incubation. Microbiol Spectr 2023; 11:e0500122. [PMID: 36809027 PMCID: PMC10100889 DOI: 10.1128/spectrum.05001-22] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/29/2023] [Indexed: 02/23/2023] Open
Abstract
EUCAST rapid antimicrobial susceptibility testing (RAST) provides antibiotic susceptibility results after 4 to 8 h of incubation. This study assessed the diagnostic performance and clinical usefulness of EUCAST RAST after 4 h. This was a retrospective clinical study performed on blood cultures with Escherichia coli and Klebsiella pneumoniae complex (K. pneumoniae and Klebsiella variicola) at Karolinska University Laboratory (Stockholm, Sweden). The rate of categorized RAST results and the categorical agreement (CA) of RAST with the standard EUCAST 16-to-20-h disk diffusion (DD) method for piperacillin-tazobactam, cefotaxime, ceftazidime, meropenem, and ciprofloxacin were analyzed, as well as the utility of RAST for adjusting the empirical antibiotic therapy (EAT) and the combination of RAST with a lateral flow assay (LFA) for extended-spectrum β-lactamase (ESBL) detection. A total of 530 E. coli and 112 K. pneumoniae complex strains were analyzed, generating 2,641 and 558 readable RAST zones, respectively. RAST results categorized according to antimicrobial sensitivity/resistance (S/R) were obtained for 83.1% (2,194/2,641) and 87.5% (488/558) of E. coli and K. pneumoniae complex strains, respectively. The RAST result categorization to S/R for piperacillin-tazobactam was poor (37.2% for E. coli and 66.1% for K. pneumoniae complex). CA with the standard DD method was over 97% for all tested antibiotics. Using RAST, we detected 15/26 and 1/10 of the E. coli and K. pneumoniae complex strains that were resistant to the EAT. For patients treated with cefotaxime, RAST was used to detect 13/14 cefotaxime-resistant E. coli strains and 1/1 cefotaxime-resistant K. pneumoniae complex strain. ESBL positivity was reported the same day as blood culture positivity with RAST and LFA. EUCAST RAST provides accurate and clinically relevant susceptibility results after 4 h of incubation and can accelerate the assessment of resistance patterns. IMPORTANCE Early effective antimicrobial treatment has been shown to be crucial for improving the outcome of bloodstream infections (BSI) and sepsis. In combination with the rise of antibiotic resistance, this calls for accelerated methods for antibiotic susceptibility testing (AST) for effective treatment of BSI. This study assesses EUCAST RAST, an AST method that yields results in 4, 6, or 8 h after blood culture positivity. We analyzed a high number of clinical samples of Escherichia coli and Klebsiella pneumoniae complex strains and confirm that the method delivers reliable results after 4 h of incubation for the relevant antibiotics for treating E. coli and K. pneumoniae complex bacteremia. Furthermore, we conclude that it is an important tool for antibiotic treatment decision-making and early detection of ESBL-producing isolates.
Collapse
Affiliation(s)
- Anna Ekwall-Larson
- Department of Clinical Microbiology, Karolinska University Hospital, Huddinge, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| | - Inga Fröding
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
- Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden
| | - Berivan Mert
- Department of Clinical Microbiology, Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Anna Åkerlund
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Linköping University Hospital, Linköping, Sweden
- Division of Clinical Microbiology, Linköping University Hospital, Linköping, Sweden
| | - Volkan Özenci
- Department of Clinical Microbiology, Karolinska University Hospital, Huddinge, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Microbiology, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
9
|
Sugiharto VA, Gatrell SK, Chen HW, Blazek GR, Cherry AM, Schilling M. Performance Evaluation of Five Rapid At-Home COVID-19 Antigen Tests against the Omicron Variant. Microbiol Spectr 2023; 11:e0228622. [PMID: 36519888 PMCID: PMC9927253 DOI: 10.1128/spectrum.02286-22] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rapid coronavirus disease 2019 (COVID-19) antigen tests can be used to aid in quickly identifying positive cases, which can help mitigate the spread of COVID-19 infection. Using previously characterized Omicron-positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), non-Omicron-positive SARS-CoV-2, and negative samples, we evaluated five brands of at-home rapid COVID-19 antigen tests (On/Go at-home COVID-19 rapid antigen self-test, iHealth COVID-19 antigen rapid test, QuickVue SARS antigen test, Abbott BinaxNOW COVID-19 card home test, and InBios SCoV-2 Ag detect rapid self-test). Our results showed that these rapid tests had similar levels of sensitivity to Omicron and non-Omicron variants (On/Go, 76.4% and 71.0%; iHealth, 73.0% and 71.0%; QuickVue, 84.3% and 74.3%; BinaxNOW, 69.7% and 71.0%; and InBios, 66.3% and 64.5%, respectively). In conclusion, rapid COVID-19 antigen tests can continue to be used as part of public health measures to combat the spread of the Omicron variant, as their sensitivity was not significantly affected. IMPORTANCE The emergence of the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to mutations as part of the virus evolution process. These mutations might affect the sensitivity of diagnostic tests that are currently being used to detect the virus. Because rapid coronavirus disease 2019 (COVID-19) antigen tests are commonly used in the general population, it is important to assess their performance in detecting the Omicron variant. Here, we compared the performance of five brands of rapid tests against Omicron and non-Omicron variants using nasopharyngeal swab samples in viral transport media. Our result found no difference in their performance, suggesting no reduction in sensitivity when used to detect the Omicron variant.
Collapse
Affiliation(s)
- Victor A. Sugiharto
- Naval Medical Research Center, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation, Bethesda, Maryland, USA
| | - Stephanie K. Gatrell
- Naval Medical Research Center, Silver Spring, Maryland, USA
- Leidos, Reston, Virginia, USA
| | - Hua-Wei Chen
- Naval Medical Research Center, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation, Bethesda, Maryland, USA
| | - Gabrielle R. Blazek
- Naval Medical Research Center, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation, Bethesda, Maryland, USA
| | - Amanda M. Cherry
- Naval Medical Research Center, Silver Spring, Maryland, USA
- Leidos, Reston, Virginia, USA
| | | |
Collapse
|
10
|
Bartosh AV, Sotnikov DV, Zherdev AV, Dzantiev BB. Handling Detection Limits of Multiplex Lateral Flow Immunoassay by Choosing the Order of Binding Zones. Micromachines (Basel) 2023; 14:333. [PMID: 36838034 PMCID: PMC9965744 DOI: 10.3390/mi14020333] [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: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Changes in the limits of detection (LODs) for a multiplex lateral flow immunoassay (LFIA) caused by different locations of the binding zone on the test strips were studied. Due to the non-equilibrium conditions of the immune reactions in LFIAs, their analytical parameters are susceptible to the binding constants of antigen-antibody reactions and assay duration. Consequently, the integration of several tests into one multiplex assay can cause a significant worsening of the sensitivity. In this study, we propose a simple methodology for the determination of the best arrangement of binding zones, which takes into account the binding constants for immunoreagents. LFIAs of four mycotoxins, namely, aflatoxin B1, deoxynivalenol, T-2 toxin, and ochratoxin A, were integrated into a multiplex test strip. An enzyme-linked immunosorbent assay was applied to determine the equilibrium and kinetic constants of the immunoreactants for each analyte. It was found that the arrangement of binding zones with a descending order of the equilibrium association constants was optimal and provided both lower detection limits and a more uniform coloration. The selected position of the binding zones allowed decreasing the LODs down to 2 and 27 times for ochratoxin A and deoxynivalenol, respectively. The proposed approach can be applied to multiplex LFIAs for different analytes.
Collapse
|
11
|
Meltzer L, Amit S, Gilboa M, Tal I, Mechnik B, Irony A, Engelrad H, Epstein A, Frenkel-Nir Y, Levy Y, Kreiss Y, Regev-Yochay G. The Use of Rapid COVID-19 Antigen Test in the Emergency Department as a Decision-Support Tool. Microorganisms 2023; 11:microorganisms11020284. [PMID: 36838249 PMCID: PMC9961521 DOI: 10.3390/microorganisms11020284] [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: 11/28/2022] [Revised: 01/04/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
The emergency department (ED) is the initial point of contact between hospital staff and patients potentially infected with SARS-CoV-2, thus, prevention of inadvertent exposure to other patients is a top priority. We aimed to assess whether the introduction of antigen-detecting rapid diagnostic tests (Ag-RDTs) to the ED affected the likelihood of unwanted SARS-CoV-2 exposures. In this retrospective single-center study, we compared the rate of unwarranted exposure of uninfected adult ED patients to SARS-CoV-2 during two separate research periods; one before Ag-RDTs were introduced, and one with Ag-RDT used as a decision-support tool. The introduction of Ag-RDTs to the ED significantly decreased the relative risk of SARS-CoV-2-negative patients being incorrectly assigned to the COVID-19 designated site ("red ED"), by 97%. There was no increase in the risk of SARS-CoV-2-positive patients incorrectly assigned to the COVID-19-free site ("green ED"). In addition, duration of ED admission was reduced in both the red and the green ED. Therefore, implementing the Ag-RDT-based triage protocol proved beneficial in preventing potential COVID-19 nosocomial transmission.
Collapse
Affiliation(s)
- Lilac Meltzer
- Infection Control & Prevention Unit, Sheba Medical Center, Ramat Gan 52621, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Sharon Amit
- Clinical Microbiology, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Mayan Gilboa
- Infection Control & Prevention Unit, Sheba Medical Center, Ramat Gan 52621, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ilana Tal
- Infection Control & Prevention Unit, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Bella Mechnik
- Infection Control & Prevention Unit, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Avi Irony
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Emergency Department, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Hindi Engelrad
- Emergency Department, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Avi Epstein
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Emergency Department, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Yael Frenkel-Nir
- The General Management, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Yuval Levy
- The General Management, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Yitshak Kreiss
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- The General Management, Sheba Medical Center, Ramat Gan 52621, Israel
| | - Gili Regev-Yochay
- Infection Control & Prevention Unit, Sheba Medical Center, Ramat Gan 52621, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Correspondence: ; Tel.: +97-25-2666-6197
| |
Collapse
|
12
|
Giacobbe DR, Crea F, Morici P, Magnasco L, Di Pilato V, Briano F, Willison E, Pincino R, Dettori S, Tutino S, Esposito S, Coppo E, Dentone C, Portunato F, Mikulska M, Robba C, Vena A, Battaglini D, Brunetti I, Ball L, Pelosi P, Marchese A, Bassetti M. T2Bacteria and T2Resistance Assays in Critically Ill Patients with Sepsis or Septic Shock: A Descriptive Experience. Antibiotics (Basel) 2022; 11:antibiotics11121823. [PMID: 36551480 PMCID: PMC9774778 DOI: 10.3390/antibiotics11121823] [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: 10/27/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The use of rapid molecular tests may anticipate the identification of causative agents and resistance determinants in the blood of critically ill patients with sepsis. From April to December 2021, all intensive care unit patients with sepsis or septic shock who were tested with the T2Bacteria and T2Resistance assays were included in a retrospective, single center study. The primary descriptive endpoints were results of rapid molecular tests and concomitant blood cultures. Overall, 38 combinations of T2Bacteria and T2Resistance tests were performed. One or more causative agent(s) were identified by the T2Bacteria assay in 26% of episodes (10/38), whereas negative and invalid results were obtained in 66% (25/38) and 8% (3/38) of episodes, respectively. The same pathogen detected by the T2Bacteria test grew from blood cultures in 30% of cases (3/10). One or more determinant(s) of resistance were identified by the T2Resistance assay in 11% of episodes (4/38). Changes in therapy based on T2Bacteria and/or T2Resistance results occurred in 21% of episodes (8/38). In conclusion, T2Bacteria/T2Resistance results can influence early treatment decisions in critically ill patients with sepsis or septic shock in real-life practice. Large, controlled studies remain necessary to confirm a favorable impact on patients' outcomes and antimicrobial stewardship interventions.
Collapse
Affiliation(s)
- Daniele Roberto Giacobbe
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy
- Infectious Diseases Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
- Correspondence:
| | - Francesca Crea
- Microbiology Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Paola Morici
- Microbiology Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Laura Magnasco
- Infectious Diseases Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132 Genoa, Italy
| | - Federica Briano
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy
- Infectious Diseases Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
- Ospedale San Paolo—ASL 2 Savonese, 17100 Savona, Italy
| | - Edward Willison
- Microbiology Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Rachele Pincino
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy
- Infectious Diseases Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
- Ospedale di Sanremo—ASL 1 Imperiese, 18038 Sanremo, Italy
| | - Silvia Dettori
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy
- Infectious Diseases Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Stefania Tutino
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy
- Infectious Diseases Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Simone Esposito
- Microbiology Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Erika Coppo
- Microbiology Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Chiara Dentone
- Infectious Diseases Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Federica Portunato
- Infectious Diseases Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Malgorzata Mikulska
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy
- Infectious Diseases Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Chiara Robba
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132 Genoa, Italy
- Anesthesia and Intensive Care, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Antonio Vena
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy
- Infectious Diseases Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Denise Battaglini
- Anesthesia and Intensive Care, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Iole Brunetti
- Anesthesia and Intensive Care, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Lorenzo Ball
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132 Genoa, Italy
- Anesthesia and Intensive Care, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Paolo Pelosi
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132 Genoa, Italy
- Anesthesia and Intensive Care, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| | - Anna Marchese
- Microbiology Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132 Genoa, Italy
| | - Matteo Bassetti
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy
- Infectious Diseases Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, 16132 Genoa, Italy
| |
Collapse
|
13
|
Herbert C, Broach J, Heetderks W, Qashu F, Gibson L, Pretz C, Woods K, Kheterpal V, Suvarna T, Nowak C, Lazar P, Ayturk D, Barton B, Achenbach C, Murphy R, McManus D, Soni A. Feasibility of At-Home Serial Testing Using Over-the-Counter SARS-CoV-2 Tests With a Digital Smartphone App for Assistance: Longitudinal Cohort Study. JMIR Form Res 2022; 6:e35426. [PMID: 36041004 PMCID: PMC9580993 DOI: 10.2196/35426] [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: 12/03/2021] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The ongoing SARS-CoV-2 pandemic necessitates the development of accurate, rapid, and affordable diagnostics to help curb disease transmission, morbidity, and mortality. Rapid antigen tests are important tools for scaling up testing for SARS-CoV-2; however, little is known about individuals' use of rapid antigen tests at home and how to facilitate the user experience. OBJECTIVE This study aimed to describe the feasibility and acceptability of serial self-testing with rapid antigen tests for SARS-CoV-2, including need for assistance and the reliability of self-interpretation. METHODS A total of 206 adults in the United States with smartphones were enrolled in this single-arm feasibility study in February and March 2021. All participants were asked to self-test for COVID-19 at home using rapid antigen tests daily for 14 days and use a smartphone app for testing assistance and to report their results. The main outcomes were adherence to the testing schedule, the acceptability of testing and smartphone app experiences, and the reliability of participants versus study team's interpretation of test results. Descriptive statistics were used to report the acceptability, adherence, overall rating, and experience of using the at-home test and MyDataHelps app. The usability, acceptability, adherence, and quality of at-home testing were analyzed across different sociodemographic, age, and educational attainment groups. RESULTS Of the 206 enrolled participants, 189 (91.7%) and 159 (77.2%) completed testing and follow-up surveys, respectively. In total, 51.3% (97/189) of study participants were women, the average age was 40.7 years, 34.4% (65/189) were non-White, and 82% (155/189) had a bachelor's degree or higher. Most (n=133/206, 64.6%) participants showed high testing adherence, meaning they completed over 75% of the assigned tests. Participants' interpretations of test results demonstrated high agreement (2106/2130, 98.9%) with the study verified results, with a κ score of 0.29 (P<.001). Participants reported high satisfaction with self-testing and the smartphone app, with 98.7% (157/159) reporting that they would recommend the self-test and smartphone app to others. These results were consistent across age, race/ethnicity, and gender. CONCLUSIONS Participants' high adherence to the recommended testing schedule, significant reliability between participants and study staff's test interpretation, and the acceptability of the smartphone app and self-test indicate that self-tests for SARS-CoV-2 with a smartphone app for assistance and reporting is a highly feasible testing modality among a diverse population of adults in the United States.
Collapse
Affiliation(s)
- Carly Herbert
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - John Broach
- Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States.,UMass Memorial Medical Center, Worcester, MA, United States
| | - William Heetderks
- National Institute of Biomedical Imaging and Bioengineering, Bethesda, MD, United States
| | - Felicia Qashu
- National Institutes of Health, Bethesda, MD, United States
| | - Laura Gibson
- Division of Infectious Disease and Immunology, Departments of Medicine and Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Caitlin Pretz
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Kelsey Woods
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | | | | | | | - Peter Lazar
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Didem Ayturk
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Bruce Barton
- Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Chad Achenbach
- Division of Infectious Disease, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Robert Murphy
- Division of Infectious Disease, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - David McManus
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States.,Department of Cardiology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Apurv Soni
- Program in Digital Medicine, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States.,Department of Population and Quantitative Health Sciences, University of Massachusetts Chan Medical School, Worcester, MA, United States
| |
Collapse
|
14
|
Sotiropoulos C, Loulelis V, Mastorakou A, Adamopoulou E, Kortesas T, Dimitropoulou A, Blika E, Papadimitriou-Olivgeri I, Binenbaum I. The Impact of the Patras Carnival on the Course of the COVID-19 Pandemic and the Outbreak of Influenza A: A Multicenter Cross-Sectional Study. Vaccines (Basel) 2022; 10:vaccines10091484. [PMID: 36146563 PMCID: PMC9502820 DOI: 10.3390/vaccines10091484] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 01/04/2023] Open
Abstract
Background: We investigated the impact of the indoor mass gathering of young people during the Patras Carnival in Greece on the course of the COVID-19 pandemic and the influenza A epidemic. Materials and Methods: For influenza A, we tested 331 subjects with high fever (>38 °C), who arrived at five separate private laboratories over a two-week period after the carnival, via rapid test. One hundred and eighty-eight of them were young adults (17−35 years old), all unvaccinated against influenza A but all immunized against SARS-CoV-2, either through vaccination or previous infection. For the SARS-CoV-2 pandemic, we tested 2062 subjects at two time periods, two weeks before and two weeks after the carnival, also via rapid test. Additionally, we examined 42 samples positive for influenza A and 51 samples positive for SARS-CoV-2 for the possibility of co-infection via molecular testing (i.e., RT-PCR). Results: 177/331 (53.5%) subjects tested positive for influenza A, and 109/177 (61.6%) of the positive subjects were young adults, and 93/109 (85.3%) of these subjects were tested in the first week after the carnival. Additionally, 42 samples of those subjects were molecularly tested, and 5 were found negative for influenza A but positive for SARS-CoV-2. Regarding the SARS-CoV-2 pandemic, the increase in the positivity index for young adults between the pre-carnival and post-carnival periods was moderate. Conclusions: Our study indicates that the indoor mass gathering of young people during the carnival contributed to the outbreak of an influenza A epidemic and had a moderate but not statistically significant impact on the course of the SARS-CoV-2 pandemic, corroborating the crucial role of vaccination against the epidemic’s waves. It also showed the need for the use of high-quality rapid tests for their management.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Eleni Blika
- Loulelis Private Laboratory, 26221 Patras, Greece
| | | | - Ilona Binenbaum
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National and Kapodistrian University of Athens, 11527 Athens, Greece
| |
Collapse
|
15
|
LeBlanc JJ, McCracken GR, Goodall B, Hatchette TF, Barrett L, Ross J, Davidson RJ, Patriquin G. Avoiding False-Positive SARS-CoV-2 Rapid Antigen Test Results with Point-of-Care Molecular Testing on Residual Test Buffer. Microbiol Spectr 2022; 10:e0063922. [PMID: 35863036 PMCID: PMC9430663 DOI: 10.1128/spectrum.00639-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 02/18/2022] [Accepted: 06/22/2022] [Indexed: 12/01/2022] Open
Abstract
Antigen-based rapid diagnostic tests (Ag-RDTs) have been widely used for the detection of SARS-CoV-2 during the coronavirus disease 2019 (COVID-19) pandemic. In settings of low disease prevalence, such as asymptomatic community testing, national guidelines recommend confirmation of positive Ag-RDT results with a nucleic acid amplification test (NAAT). This often requires patients to be recalled for repeat specimen recollection and subsequent testing in reference laboratories. This project assessed the use of a point-of-care molecular NAAT for SARS-CoV-2 detection (i.e., ID NOW), which was performed on-site at a volunteer-led asymptomatic community testing site on the residual test buffer (RTB) from positive Ag-RDTs. The ID NOW NAAT assay was performed on RTB from two Ag-RDTs: the Abbott Panbio and BTNX Rapid Response assays. Results of ID NOW were compared to real-time RT-PCR at a reference laboratory. Along with investigations into the clinical performance of ID NOW on RTB, analytical specificity was assessed with a panel of various respiratory organisms. Of the Ag-RDTs results evaluated, all 354 Ag-RDTs results characterized as true positives by RT-PCR were accurately identified with ID NOW testing of RTB. No SARS-CoV-2 detections by ID NOW were observed from 10 specimens characterized as false-positive Ag-RDTs, or from contrived specimens with various respiratory organisms. The use of on-site molecular testing on RTB provides a suitable option for rapid confirmatory testing of positive Ag-RDTs, thereby obviating the need for specimen recollection for molecular testing at local reference laboratories. IMPORTANCE During the COVID-19 pandemic, rapid antigen tests have been widely used for the detection of SARS-CoV-2. These simple devices allow rapid test results. However, false-positive results may occur. As such, individuals with positive rapid tests often must return to testing centers to have a second swab collected, which is then transported to a specialized laboratory for confirmation using molecular tests. As an alternative to requiring a repeat visit and a prolonged turn-around time for result confirmation, this project evaluated whether the leftover material from rapid antigen tests could be confirmed directly on a portable point-of-care molecular instrument. Using this approach, molecular confirmation of positive antigen tests could be performed in less than 15 min, and the results were equivalent to laboratory-based confirmation. This procedure eliminates the need for individuals to return to testing centers following a positive rapid antigen test and ensures accurate antigen test results through on-site confirmation.
Collapse
Affiliation(s)
- Jason J. LeBlanc
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Nova Scotia Health, Halifax, Nova Scotia, Canada
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Gregory R. McCracken
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Barbara Goodall
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Todd F. Hatchette
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Nova Scotia Health, Halifax, Nova Scotia, Canada
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lisa Barrett
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Nova Scotia Health, Halifax, Nova Scotia, Canada
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John Ross
- Praxes Medical Group, Halifax, Nova Scotia, Canada
| | - Ross J. Davidson
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Nova Scotia Health, Halifax, Nova Scotia, Canada
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Glenn Patriquin
- Department of Pathology and Laboratory Medicine, Division of Microbiology, Nova Scotia Health, Halifax, Nova Scotia, Canada
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| |
Collapse
|
16
|
Koga P, Maluf M, Nunes F, Campos J, Gazarini L, Borghoff T, Libanori G, Martino M. Comparison of the SARS-CoV-2 BD Veritor Nasal Antigen Test with Nasopharyngeal Reverse Transcription-PCR in Symptomatic Patients. Microbiol Spectr 2022;:e0019022. [PMID: 36036635 DOI: 10.1128/spectrum.00190-22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
This study evaluated the BD Veritor system for rapid detection of SARS-CoV-2, an immunochromatographic point-of-care test, by comparing it with a standard reverse transcription-PCR (RT-PCR) methodology using samples from symptomatic patients. Samples from 146 symptomatic and 2 asymptomatic patients between the 1st and the 40th day of infection were evaluated. The nasopharyngeal and/or oropharyngeal swabs were inserted in a tube containing 0.9% saline solution and stored at refrigerator temperature until the moment of use. The samples were first tested with the Xpert Xpress SARS-CoV-2 (GeneXpert) kit (RT-PCR method), and the cycle thresholds (CTs) for the E and N2 genes encoding the SARS-CoV-2 envelope and nucleoprotein, respectively, were established. Subsequently, the same samples were tested using the Veritor rapid test. We analyzed the CTs of the N2 gene, which is detected in both methodologies, and observed sensitivities of 100%, 98.8%, 89.6%, and 82.7% for the CTs of <25, <27, and <30 and all the CTs, respectively. The greatest sensitivity was observed when we performed the test on patients within 5 days of symptom onset. The BD Veritor system’s workflow is simple and fast, taking approximately 16 min from sample preparation to obtaining the test result. In addition to its satisfactory sensitivity, with results that correlate with those of the RT-PCR, the BD Veritor analyzer instrument reduces the subjectivity of unaided visual readings and consequent potential variation in result interpretation. Therefore, our results showed that the BD Veritor diagnostic test can provide a rapid and accurate diagnosis for SARS-CoV-2. IMPORTANCE This study provides important and useful information, especially for diagnostic laboratories, since the results show that the BD Veritor system can provide a fast and safe point-of-care antigen diagnostic test for rapid detection of COVID-19 that has high sensitivity, reproducibility, and accuracy.
Collapse
|
17
|
Uejima Y, Suganuma E, Ohnishi T, Takei H, Furuichi M, Sato S, Kawano Y, Kitajima I, Niimi H. Prospective Study of the Detection of Bacterial Pathogens in Pediatric Clinical Specimens Using the Melting Temperature Mapping Method. Microbiol Spectr 2022; 10:e0019822. [PMID: 35674438 PMCID: PMC9241829 DOI: 10.1128/spectrum.00198-22] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/17/2022] [Indexed: 11/20/2022] Open
Abstract
The melting temperature (Tm) mapping method is a novel technique that uses seven primer sets without sequencing to detect dominant bacteria. This method can identify pathogenic bacteria in adults within 3 h of blood collection without using conventional culture methods. However, no studies have examined whether pathogenic bacteria can be detected in clinical specimens from pediatric patients with bacterial infections. Here, we designed a new primer set for commercial use, constructed a database with more bacterial species, and examined the agreement rate of bacterial species in vitro. Moreover, we investigated whether our system could detect pathogenic bacteria from pediatric patients using the Tm mapping method and compared the detection rates of the Tm mapping and culture methods. A total of 256 pediatric clinical specimens from 156 patients (94 males and 62 females; median age, 2 years [<18 years of age]) were used. The observed concordance rates between the Tm mapping method and the culture method for both positive and negative samples were 76.4% (126/165) in blood samples and 79.1% (72/91) in other clinical specimens. The Tm mapping detection rate was higher than that of culture using both blood and other clinical specimens. In addition, using the Tm mapping method, we identified causative bacteria in pediatric clinical specimens quicker than when using blood cultures. Hence, the Tm mapping method could be a useful adjunct for diagnosing bacterial infections in pediatric patients and may be valuable in antimicrobial stewardship for patients with bacterial infections, especially in culture-negative cases. IMPORTANCE This study provides novel insights regarding the use of the melting temperature (Tm) mapping method to identify the dominant bacteria in samples collected from pediatric patients. We designed a new set of primers for commercial use and developed a database of different bacteria that can be identified using these primers. We show that the Tm mapping method could identify bacteria from blood samples and other clinical specimens. Moreover, we provide evidence that the Tm mapping method has a higher detection rate than that of the culture-based methods and can achieve a relatively high agreement rate. We believe that our study makes a significant contribution to this field because rapid identification of the source of bacterial infections can drastically improve patient outcomes and impede the development of antibiotic-resistant bacteria.
Collapse
Affiliation(s)
- Yoji Uejima
- Division of Infectious Diseases and Immunology, Saitama Children’s Medical Center, Saitama, Japan
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Eisuke Suganuma
- Division of Infectious Diseases and Immunology, Saitama Children’s Medical Center, Saitama, Japan
| | - Takuma Ohnishi
- Division of Infectious Diseases and Immunology, Saitama Children’s Medical Center, Saitama, Japan
| | - Haruka Takei
- Division of Infectious Diseases and Immunology, Saitama Children’s Medical Center, Saitama, Japan
| | - Mihoko Furuichi
- Division of Infectious Diseases and Immunology, Saitama Children’s Medical Center, Saitama, Japan
| | - Satoshi Sato
- Division of Infectious Diseases and Immunology, Saitama Children’s Medical Center, Saitama, Japan
| | - Yutaka Kawano
- Division of Infectious Diseases and Immunology, Saitama Children’s Medical Center, Saitama, Japan
| | - Isao Kitajima
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Faculty of Medicine, Academic Assembly, University of Toyama, Toyama, Japan
| |
Collapse
|
18
|
Hayer JJ, Heinemann C, Schulze-Dieckhoff BG, Steinhoff-Wagner J. A risk-oriented evaluation of biofilm and other influencing factors on biological quality of drinking water for dairy cows. J Anim Sci 2022; 100:skac112. [PMID: 35390153 PMCID: PMC9115896 DOI: 10.1093/jas/skac112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 12/02/2021] [Accepted: 04/01/2022] [Indexed: 11/12/2022] Open
Abstract
Despite the importance of livestock drinking water quality on animal physiology, welfare, and performance, influences such as biofilm formation on trough surfaces on microbial water quality are rarely researched. The objective of this study was to assess the microbial quality of water offered to lactating dairy cows and identify risk factors for poor water quality. We further aimed to determine the impact of biofilm formation on water quality and evaluate rapid test systems to score the hygiene status of dairy troughs on the farm. A total of 105 troughs located on 24 typical Western German dairy farms were sampled. Samples of livestock drinking water and biofilm were analyzed for aerobic total viable count (TVC), coliform count (CC), Escherichia coli, methicillin-resistant Staphylococcus aureus (MRSA), and other bacteria resistant to 3rd generation cephalosporins (CRB). Surface protein- and adenosine triphosphate (ATP)-rapid tests were evaluated to detect biofilm formation. The influence of 22 selected fixed and variable trough characteristics on impaired livestock drinking water quality was evaluated by calculating odds ratios. The average TVC, CC, and E. coli counts were 4.4 ± 0.06 (mean ± SD), 1.7 ± 0.1, and 0.6 ± 0.1 log10 cfu per mL, respectively. CC was detectable in 94.3% of all water samples and E. coli in 48.6%. MRSA was found in pooled livestock drinking water samples of a single farm and CRB on three farms, suggesting that troughs might function as a reservoir of antibiotic-resistant bacteria, thereby contributing to an exchange of antibiotic-resistant bacteria between animals. Risk factors for the impairment of at least one microbial quality criteria (TVC, CC, or E. coli) increased significantly (P < 0.05) when using high-volume troughs, other trough materials than stainless steel, a lower distance to the milking parlor, heavy visible soiling, biofilm formation, and high ambient and high water temperatures. CC (r = 0.46; P < 0.001) and E. coli (r = 0.31; P < 0.01) of water samples correlated with their equivalent in biofilm and with the results of rapid tests on trough surfaces (0.31 > r > 0.19; P < 0.05). Addressing the identified risk factors could be an approach to ensure sufficient biological quality of livestock drinking water.
Collapse
Affiliation(s)
- Jason J Hayer
- Institute of Animal Science, University of Bonn, 53115 Bonn, Germany
| | - Céline Heinemann
- Institute of Animal Science, University of Bonn, 53115 Bonn, Germany
| | | | | |
Collapse
|
19
|
Lee KS, Lim HJ, Kim K, Park YG, Yoo JW, Yong D. Rapid Bacterial Detection in Urine Using Laser Scattering and Deep Learning Analysis. Microbiol Spectr 2022;:e0176921. [PMID: 35234514 DOI: 10.1128/spectrum.01769-21] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Images of laser scattering patterns generated by bacteria in urine are promising resources for deep learning. However, floating bacteria in urine produce dynamic scattering patterns and require deep learning of spatial and temporal features. We hypothesized that bacteria with variable bacterial densities and different Gram staining reactions would generate different speckle images. After deep learning of speckle patterns generated by various densities of bacteria in artificial urine, we validated the model in an independent set of clinical urine samples in a tertiary hospital. Even at a low bacterial density cutoff (1,000 CFU/mL), the model achieved a predictive accuracy of 90.9% for positive urine culture. At a cutoff of 50,000 CFU/mL, it showed a better accuracy of 98.5%. The model achieved satisfactory accuracy at both cutoff levels for predicting the Gram staining reaction. Considering only 30 min of analysis, our method appears as a new screening tool for predicting the presence of bacteria before urine culture. IMPORTANCE This study performed deep learning of multiple laser scattering patterns by the bacteria in urine to predict positive urine culture. Conventional urine analyzers have limited performance in identifying bacteria in urine. This novel method showed a satisfactory accuracy taking only 30 min of analysis without conventional urine culture. It was also developed to predict the Gram staining reaction of the bacteria. It can be used as a standalone screening tool for urinary tract infection.
Collapse
|
20
|
Wang Y, Zhang C, Wang J, Knopp D. Recent Progress in Rapid Determination of Mycotoxins Based on Emerging Biorecognition Molecules: A Review. Toxins (Basel) 2022; 14:toxins14020073. [PMID: 35202100 PMCID: PMC8874725 DOI: 10.3390/toxins14020073] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/14/2022] [Accepted: 01/15/2022] [Indexed: 12/12/2022] Open
Abstract
Mycotoxins are secondary metabolites produced by fungal species, which pose significant risk to humans and livestock. The mycotoxins which are produced from Aspergillus, Penicillium, and Fusarium are considered most important and therefore regulated in food- and feedstuffs. Analyses are predominantly performed by official laboratory methods in centralized labs by expert technicians. There is an urgent demand for new low-cost, easy-to-use, and portable analytical devices for rapid on-site determination. Most significant advances were realized in the field bioanalytical techniques based on molecular recognition. This review aims to discuss recent progress in the generation of native biomolecules and new bioinspired materials towards mycotoxins for the development of reliable bioreceptor-based analytical methods. After brief presentation of basic knowledge regarding characteristics of most important mycotoxins, the generation, benefits, and limitations of present and emerging biorecognition molecules, such as polyclonal (pAb), monoclonal (mAb), recombinant antibodies (rAb), aptamers, short peptides, and molecularly imprinted polymers (MIPs), are discussed. Hereinafter, the use of binders in different areas of application, including sample preparation, microplate- and tube-based assays, lateral flow devices, and biosensors, is highlighted. Special focus, on a global scale, is placed on commercial availability of single receptor molecules, test-kits, and biosensor platforms using multiplexed bead-based suspension assays and planar biochip arrays. Future outlook is given with special emphasis on new challenges, such as increasing use of rAb based on synthetic and naïve antibody libraries to renounce animal immunization, multiple-analyte test-kits and high-throughput multiplexing, and determination of masked mycotoxins, including stereoisomeric degradation products.
Collapse
Affiliation(s)
- Yanru Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.W.); (C.Z.)
| | - Cui Zhang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.W.); (C.Z.)
| | - Jianlong Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.W.); (C.Z.)
- Correspondence: (J.W.); (D.K.)
| | - Dietmar Knopp
- Chair for Analytical Chemistry and Water Chemistry, Institute of Hydrochemistry, Technische Universitat München, Elisabeth-Winterhalter-Weg 6, D-81377 München, Germany
- Correspondence: (J.W.); (D.K.)
| |
Collapse
|
21
|
Kállai A, Kelemen M, Molnár N, Tropotei A, Hauser B, Iványi Z, Gál J, Ligeti E, Kristóf K, Lőrincz ÁM. MICy: a Novel Flow Cytometric Method for Rapid Determination of Minimal Inhibitory Concentration. Microbiol Spectr 2021; 9:e0090121. [PMID: 34878335 DOI: 10.1128/spectrum.00901-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Indexed: 12/20/2022] Open
Abstract
Early initiated adequate antibiotic treatment is essential in intensive care. Shortening the length of antibiotic susceptibility testing (AST) can accelerate clinical decision-making. Our objective was to develop a simple flow cytometry (FC)-based AST that produces reliable results within a few hours. We developed a FC-based AST protocol (MICy) and tested it on six different bacteria strains (Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, Enterococcus faecalis) in Mueller-Hinton and Luria-Bertani broth. We monitored the bacterial growth by FC to define the optimal time of AST. All bacteria were tested against 12 antibiotics and the MIC values were compared to microdilution used as reference method. McNemar and Fleiss' kappa inter-observer tests were performed to analyze the bias between the two methods. Susceptibility profiles of the two methods were also compared. We found that FC is able to detect the bacterial growth after 4-h incubation. The point-by-point comparison of MICy and microdilution resulted in exact match above 87% (2642/3024) of all measurements. The MIC values obtained by MICy and microdilution agreed over 80% (173/216) within ±1 dilution range that gives a substantial inter-observer agreement with weighted Fleiss' kappa. By using the EUCAST clinical breakpoints, we defined susceptibility profiles of MICy that were identical to microdilution in more than 92% (197/213) of the decisions. MICy resulted 8.7% major and 3.2% very major discrepancies. MICy is a new, simple FC-based AST method that produces susceptibility profile with low failure rate a workday earlier than the microdilution method. IMPORTANCE MICy is a new, simple and rapid flow cytometry based antibiotic susceptibility testing (AST) method that produces susceptibility profile a workday earlier than the microdilution method or other classical phenotypic AST methods. Shortening the length of AST can accelerate clinical decision-making as targeted antibiotic treatment improves clinical outcomes and reduces mortality, duration of artificial ventilation, and length of stay in intensive care unit. It can also reduce nursing time and costs and the spreading of antibiotic resistance. In this study, we present the workflow and methodology of MICy and compare the results produced by MICy to microdilution step by step.
Collapse
|
22
|
Goupil-Sormany I, Longtin J, Dumaresq J, Jacob-Wagner M, Bouchard F, Romero L, Harvey J, Bestman-Smith J, Provençal M, Beauchemin S, Richard V, Labbé AC. The PRONTO study: Clinical performance of ID NOW in individuals with compatible SARS-CoV-2 symptoms in walk-in centres-accelerated turnaround time for contact tracing. Can Commun Dis Rep 2021; 47:534-42. [PMID: 35018141 DOI: 10.14745/ccdr.v47i12a04] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Background This PRONTO study investigated the clinical performance of the Abbott ID NOWTM (IDN) COVID-19 diagnostic assay used at point of care and its impact on turnaround time for divulgation of test results. Methods Prospective study conducted from December 2020 to February 2021 in acute symptomatic participants presenting in three walk-in centres in the province of Québec. Results Valid paired samples were obtained from 2,372 participants. A positive result on either the IDN or the standard-of-care nucleic acid amplification test (SOC-NAAT) was obtained in 423 participants (prevalence of 17.8%). Overall sensitivity of IDN and SOC-NAAT were 96.4% (95% CI: 94.2-98.0%) and 99.1% (95% CI: 97.6-99.8), respectively; negative predictive values were 99.2% (95% CI: 98.7-99.6%) and 99.8% (95% CI: 99.5-100%), respectively. Turnaround time for positive results was significantly faster on IDN. Conclusion In our experience, IDN use in symptomatic individuals in walk-in centres is a reliable sensitive alternative to SOC-NAAT without the need for subsequent confirmation of negative results. Such deployment can accelerate contact tracing, reduce the burden on laboratories and increase access to testing.
Collapse
|
23
|
Ariyaratne M, Gunasekara P, Wajirasena PH, Rathnayake DM, Dilani D, Chathuranga T, Gomes L, Jayatunga D, Wewita S, Meegahage T, Jayasinghearachchi HS, Wijewickrama A, Malavige G, De Silva AD. Comparison of two rapid test kits with real time polymerase chain reaction for early diagnosis of dengue in Sri Lanka. J Immunoassay Immunochem 2021; 43:213-221. [PMID: 34724872 DOI: 10.1080/15321819.2021.1984252] [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: 01/11/2023]
Abstract
Dengue is among the deadliest insect-borne diseases circulating in Sri Lanka. Most of the infections that are diagnosed early are manageable. However, delays in diagnosis may cause fatalities. We evaluated the dengue NS1 antigen card and NS1 SD kit for early diagnosis of dengue using samples from 116 RT-PCR-positive patients admitted within 5 days of the fever onset. RT-PCR tests were performed as standard tests. IgM and IgG ELISA tests were carried out to identify primary and secondary infections. Of the 116 patients who tested positive for dengue using PCR, 48 were positive using NS1 antigen card and 45 were positive using NS1 SD. Patients with 100 copies or higher viral load showed a higher sensitivity in both antigen card and NS1 SD. Of 34 primary infections evaluated, 23 were positive by NS1 antigen card, while the positivity was 21 by NS1 SD. Of the 30 secondary infections evaluated, 15 were positive by NS1 antigen card while 14 by NS1 SD. Our findings showed that while the rapid tests are convenient and much easier to use than PCR, they are less sensitive and need improvement. Until then, clinical diagnosis should have more emphasis on the early diagnosis of dengue.
Collapse
Affiliation(s)
- Mhjd Ariyaratne
- Biomedical Lab-2, Department of Paraclinical Science, Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka.,Centre for Dengue Research, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Peshala Gunasekara
- Biomedical Lab-2, Department of Paraclinical Science, Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Poornima Hasanthi Wajirasena
- Biomedical Lab-2, Department of Paraclinical Science, Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka.,National Institute of Infectious Diseases, Angoda, Sri Lanka
| | - Dilini Malsha Rathnayake
- Biomedical Lab-2, Department of Paraclinical Science, Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka.,National Institute of Infectious Diseases, Angoda, Sri Lanka
| | - Desha Dilani
- Biomedical Lab-2, Department of Paraclinical Science, Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Teshan Chathuranga
- Biomedical Lab-2, Department of Paraclinical Science, Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Laksiri Gomes
- Biomedical Lab-2, Department of Paraclinical Science, Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | - Dadl Jayatunga
- Biomedical Lab-2, Department of Paraclinical Science, Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka.,National Institute of Infectious Diseases, Angoda, Sri Lanka
| | - Sjc Wewita
- Biomedical Lab-2, Department of Paraclinical Science, Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka.,National Institute of Infectious Diseases, Angoda, Sri Lanka
| | - Thilini Meegahage
- Biomedical Lab-2, Department of Paraclinical Science, Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka.,National Institute of Infectious Diseases, Angoda, Sri Lanka
| | - Himali S Jayasinghearachchi
- Biomedical Lab-2, Department of Paraclinical Science, Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| | | | - Gathsaurie Malavige
- Centre for Dengue Research, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - A D De Silva
- Biomedical Lab-2, Department of Paraclinical Science, Faculty of Medicine, Sir John Kotelawala Defence University, Ratmalana, Sri Lanka
| |
Collapse
|
24
|
Zhang Z, Pandey R, Li J, Gu J, White D, Stacey HD, Ang JC, Steinberg C, Capretta A, Filipe CDM, Mossman K, Balion C, Miller MS, Salena BJ, Yamamura D, Soleymani L, Brennan JD, Li Y. High-Affinity Dimeric Aptamers Enable the Rapid Electrochemical Detection of Wild-Type and B.1.1.7 SARS-CoV-2 in Unprocessed Saliva. Angew Chem Int Ed Engl 2021; 60:24266-24274. [PMID: 34464491 PMCID: PMC8596624 DOI: 10.1002/anie.202110819] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [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: 08/11/2021] [Indexed: 01/05/2023]
Abstract
We report a simple and rapid saliva-based SARS-CoV-2 antigen test that utilizes a newly developed dimeric DNA aptamer, denoted as DSA1N5, that specifically recognizes the spike proteins of the wildtype virus and its Alpha and Delta variants with dissociation constants of 120, 290 and 480 pM, respectively, and binds pseudotyped lentiviruses expressing the wildtype and alpha trimeric spike proteins with affinity constants of 2.1 pM and 2.3 pM, respectively. To develop a highly sensitive test, DSA1N5 was immobilized onto gold electrodes to produce an electrochemical impedance sensor, which was capable of detecting 1000 viral particles per mL in 1:1 diluted saliva in under 10 min without any further sample processing. Evaluation of 36 positive and 37 negative patient saliva samples produced a clinical sensitivity of 80.5 % and specificity of 100 % and the sensor could detect the wildtype virus as well as the Alpha and Delta variants in the patient samples, which is the first reported rapid test that can detect any emerging variant of SARS-CoV-2.
Collapse
Affiliation(s)
- Zijie Zhang
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
| | - Richa Pandey
- Department of Engineering PhysicsMcMaster UniversityCanada
| | - Jiuxing Li
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
| | - Dawn White
- Biointerfaces InstituteMcMaster UniversityCanada
| | - Hannah D. Stacey
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- McMaster Immunology Research CentreMcMaster UniversityCanada
| | - Jann C. Ang
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- McMaster Immunology Research CentreMcMaster UniversityCanada
| | | | - Alfredo Capretta
- Biointerfaces InstituteMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
| | | | - Karen Mossman
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- Department of MedicineMcMaster UniversityCanada
| | - Cynthia Balion
- Department of Pathology and Molecular MedicineMcMaster UniversityCanada
| | - Matthew S. Miller
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- McMaster Immunology Research CentreMcMaster UniversityCanada
| | | | - Deborah Yamamura
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- Department of Pathology and Molecular MedicineMcMaster UniversityCanada
| | - Leyla Soleymani
- Department of Engineering PhysicsMcMaster UniversityCanada
- School of Biomedical EngineeringMcMaster University1280 Main Street WestHamiltonOntarioL8S 4K1Canada
| | | | - Yingfu Li
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityCanada
- Biointerfaces InstituteMcMaster UniversityCanada
- Michael G. DeGroote Institute of Infectious Disease ResearchMcMaster UniversityCanada
- School of Biomedical EngineeringMcMaster University1280 Main Street WestHamiltonOntarioL8S 4K1Canada
| |
Collapse
|
25
|
Forno D, Samayoa B, Medina N, Arathoon E, Mejia CR, Gordillo R, Cedillos R, Rodas J, Ahlquist Cleveland A, Chiller T, Caceres DH. Diagnosis of fungal opportunistic infections in people living with HIV from Guatemala and El Salvador. Mycoses 2021; 64:1563-1570. [PMID: 34536307 PMCID: PMC8781144 DOI: 10.1111/myc.13368] [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: 07/11/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 01/13/2023]
Abstract
Objectives Histoplasmosis and cryptococcosis are important public health problems in people living with HIV (PLHIV) in Central America. Conventional laboratory tests, such as culture and microscopy, are not optimal; however, antigen (Ag) tests are rapid, highly sensitive, and specific for diagnosis of fungal opportunistic infections (OI). The aim of this study was to describe the results of a laboratory‐based surveillance system for histoplasmosis and cryptococcosis. Methods An observational cross‐sectional study based on laboratory surveillance, was carried out in two hospitals in Guatemala and one hospital in El Salvador, between July 2012 and December 2014. Diagnosis of histoplasmosis and cryptococcosis in PLHIV were performed by culture and Ag test. Results A total of 160 PLHIV were diagnosed with fungal OI, of which, 96 (60%) were diagnosed with histoplasmosis, 62 (39%) were with cryptococcosis, and two patients (1%) were diagnosed with both fungal diseases. Of the 160 patients analysed in this study, 94 (59%) were diagnosed using only an Ag assay. CD4 cell count data were available for 136 (85%) patients; 127 (93%) patients had a CD4 count <200; and 90 (66%) had counts <50 CD4 cells per µl. Antiretroviral therapy utilisation at diagnosis was low (33%). Seventy‐one out of 160 (44%) were co‐infected with tuberculosis or other OIs. Conclusion More than half of the patients in this study were diagnosed only by rapid laboratory Ag tests. A high per cent of the patients had advanced HIV disease.
Collapse
Affiliation(s)
- Diana Forno
- Division of Global HIV & TB at the Central America Regional Office for the Centers for Disease Control and Prevention (CDC), Guatemala City, Guatemala
| | - Blanca Samayoa
- Asociación de Salud Integral, Guatemala City, Guatemala.,Facultad de Ciencias Químicas y Farmacia, Universidad de San Carlos de Guatemala, Guatemala City, Guatemala
| | - Narda Medina
- Asociación de Salud Integral, Guatemala City, Guatemala.,Clinica Familiar "Luis Ángel García", Hospital General San Juan de Dios, Guatemala City, Guatemala
| | - Eduardo Arathoon
- Asociación de Salud Integral, Guatemala City, Guatemala.,Clinica Familiar "Luis Ángel García", Hospital General San Juan de Dios, Guatemala City, Guatemala
| | | | | | | | - Jose Rodas
- Division of Global HIV & TB at the Central America Regional Office for the Centers for Disease Control and Prevention (CDC), Guatemala City, Guatemala
| | | | - Tom Chiller
- Mycotic Diseases Branch, CDC, Atlanta, GA, USA
| | - Diego H Caceres
- Mycotic Diseases Branch, CDC, Atlanta, GA, USA.,Department of Medical Microbiology, Radboud University Medical Center and Center of Expertise in Mycology Radboudumc/CWZ, Nijmegen, The Netherlands
| |
Collapse
|
26
|
Bordbar MM, Sheini A, Hashemi P, Hajian A, Bagheri H. Disposable Paper-Based Biosensors for the Point-of-Care Detection of Hazardous Contaminations-A Review. Biosensors (Basel) 2021; 11:316. [PMID: 34562906 PMCID: PMC8464915 DOI: 10.3390/bios11090316] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/29/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
The fast detection of trace amounts of hazardous contaminations can prevent serious damage to the environment. Paper-based sensors offer a new perspective on the world of analytical methods, overcoming previous limitations by fabricating a simple device with valuable benefits such as flexibility, biocompatibility, disposability, biodegradability, easy operation, large surface-to-volume ratio, and cost-effectiveness. Depending on the performance type, the device can be used to analyze the analyte in the liquid or vapor phase. For liquid samples, various structures (including a dipstick, as well as microfluidic and lateral flow) have been constructed. Paper-based 3D sensors are prepared by gluing and folding different layers of a piece of paper, being more user-friendly, due to the combination of several preparation methods, the integration of different sensor elements, and the connection between two methods of detection in a small set. Paper sensors can be used in chromatographic, electrochemical, and colorimetric processes, depending on the type of transducer. Additionally, in recent years, the applicability of these sensors has been investigated in various applications, such as food and water quality, environmental monitoring, disease diagnosis, and medical sciences. Here, we review the development (from 2010 to 2021) of paper methods in the field of the detection and determination of toxic substances.
Collapse
Affiliation(s)
- Mohammad Mahdi Bordbar
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran 19945, Iran;
| | - Azarmidokht Sheini
- Department of Mechanical Engineering, Shohadaye Hoveizeh Campus of Technology, Shahid Chamran University of Ahvaz, Dashte Azadegan 78986, Iran;
| | - Pegah Hashemi
- Research and Development Department, Farin Behbood Tashkhis Ltd., Tehran 16471, Iran;
| | - Ali Hajian
- Institute of Sensor and Actuator Systems, TU Wien, Gusshausstrasse 27-29, 1040 Vienna, Austria;
| | - Hasan Bagheri
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran 19945, Iran;
| |
Collapse
|
27
|
Yoon SH, Kim HR, Ahn JG. Diagnostic Accuracy of Immunochromatographic Tests for the Detection of Norovirus in Stool Specimens: a Systematic Review and Meta-Analysis. Microbiol Spectr 2021; 9:e0046721. [PMID: 34232095 PMCID: PMC8552764 DOI: 10.1128/spectrum.00467-21] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 01/11/2023] Open
Abstract
Noroviruses are the leading cause of acute gastroenteritis in all age groups and constitute a major health and economic burden worldwide. This systematic review and meta-analysis aimed to determine the diagnostic accuracy of immunochromatographic tests (ICTs) for the detection of norovirus in stool specimens, which has not been performed previously. In this systematic review and meta-analysis (registered on PROSPERO, CRD42020186911), we searched Medline/PubMed, Embase, Cochrane Library, and Web of Science for all studies published up to 16 May 2020. The values for sensitivity, specificity, positive likelihood ratio (LR+), negative likelihood ratio (LR-), and diagnostic odds ratio (DOR) of ICTs with 95% confidence interval (CI) were pooled using a bivariate random-effects model. The summary receiver operating characteristic curve and area under the curve were used to summarize overall test accuracy. We included 43 studies describing 7,428 samples. The overall estimates of sensitivity, specificity, LR+, LR-, DOR, and accuracy of ICT for diagnosing norovirus were 0.61 (95% CI, 0.54 to 0.67), 0.97 (95% CI, 0.95 to 0.98), 17.08 (95% CI, 11.15 to 26.18), 0.40 (95% CI, 0.34 to 0.46), 53.9 (95% CI, 31.32 to 92.78), and 0.928, respectively. Significant differences in pooled sensitivities were noted between age groups and in pooled DOR and LR+ between genogroups of included samples. ICT provides low sensitivity but high specificity and accuracy for detecting norovirus. Thus, an ICT for norovirus can be a rapid and convenient way for identifying patients early; however, a negative result cannot rule out norovirus infection and should be confirmed by a reference test.
Collapse
Affiliation(s)
- Seo Hee Yoon
- Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hye Rim Kim
- Biostatistics Collaboration Unit, Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Gyun Ahn
- Department of Pediatrics, Severance Children’s Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
28
|
Trevisan C, Damme IV, Ngowi B, Schmidt V, Stelzle D, Møller KS, Kabululu M, Makasi CE, Magnussen P, Bottieau E, Abatih E, Johansen MV, Ngowi H, Ndawi B, Mwape KE, Zulu G, Dorny P, Winkler AS, Gabriël S. Trial Design of a Prospective Multicenter Diagnostic Accuracy Study of a Point-of-Care Test for the Detection of Taenia solium Taeniosis and Neurocysticercosis in Hospital-Based Settings in Tanzania. Diagnostics (Basel) 2021; 11:diagnostics11091528. [PMID: 34573870 PMCID: PMC8470609 DOI: 10.3390/diagnostics11091528] [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: 07/08/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/20/2022] Open
Abstract
Taenia solium diagnosis is challenging as trained personnel, good diagnostic tools, and infrastructure is lacking in resource-poor areas. This paper aims to describe the study trial design adopted to evaluate a newly developed rapid point-of-care test that simultaneously detects taeniosis and neurocysticercosis (TS POC) in three district hospitals in Tanzania. The two-stage design included three types of patients: patients with specific neurological signs and symptoms (group 1); patients with complaints compatible with intestinal worm infections (group 2); patients with other symptom(s) (group 3). For group 1, all patients were tested using the TS POC test (stage 1), after which all positive, and a subset of negative, patients were selected for laboratory reference tests, clinical examination, and a brain computed tomography (CT) scan (stage 2). For groups 2 and 3, a similar design was adopted, but clinical examination and a brain CT scan (stage 2) were only performed in patients who were TS POC test-positive for cysticercosis. Due to the lack of a gold standard, a Bayesian approach was used to determine test accuracy for taeniosis and cysticercosis. For neurocysticercosis, a composite case definition was used as the reference standard. If successful, this study will help the future developments (commercialization and implementation) of the rapid test and improve patient management and disease prevention.
Collapse
Affiliation(s)
- Chiara Trevisan
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium;
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium;
- Correspondence: (C.T.); (S.G.)
| | - Inge Van Damme
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium;
| | - Bernard Ngowi
- National Institute for Medical Research, Muhimbili Medical Research Centre Dar es Salaam, Dar es Salaam 11101, Tanzania; (B.N.); (C.E.M.)
- Department of Public Health, University of Dar es Salaam Tanzania, Dar es Salaam 65015, Tanzania
| | - Veronika Schmidt
- Department of Neurology, Center for Global Health, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; (V.S.); (D.S.); (A.S.W.)
- Centre for Global Health, Institute of Health and Society, Faculty of Medicine, University of Oslo, 0450 Oslo, Norway
| | - Dominik Stelzle
- Department of Neurology, Center for Global Health, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; (V.S.); (D.S.); (A.S.W.)
- Chair of Epidemiology, Department of Sport and Health Sciences, Technical University of Munich, 80809 Munich, Germany
| | - Karen Schou Møller
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark;
| | - Mwemezi Kabululu
- Tanzania Livestock Research Institute (TALIRI)-Uyole, Mbeya P.O. Box 6191, Tanzania;
| | - Charles E. Makasi
- National Institute for Medical Research, Muhimbili Medical Research Centre Dar es Salaam, Dar es Salaam 11101, Tanzania; (B.N.); (C.E.M.)
| | - Pascal Magnussen
- Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark;
| | - Emmanuel Bottieau
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium;
| | - Emmanuel Abatih
- Department of Applied Mathematics, Computer Sciences and Statistics, Faculty of Sciences, Ghent University, 9000 Ghent, Belgium;
| | | | - Helena Ngowi
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro P.O. Box 3021, Tanzania;
| | | | - Kabemba E. Mwape
- Department of Clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (K.E.M.); (G.Z.)
| | - Gideon Zulu
- Department of Clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (K.E.M.); (G.Z.)
- Eastern Provincial Health Office, Ministry of Health, Lusaka 30205, Zambia
| | - Pierre Dorny
- Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium;
| | - Andrea S. Winkler
- Department of Neurology, Center for Global Health, Klinikum rechts der Isar, Technical University of Munich, 81675 Munich, Germany; (V.S.); (D.S.); (A.S.W.)
- Centre for Global Health, Institute of Health and Society, Faculty of Medicine, University of Oslo, 0450 Oslo, Norway
| | - Sarah Gabriël
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium;
- Correspondence: (C.T.); (S.G.)
| | | |
Collapse
|
29
|
Betsch C, Sprengholz P, Siegers R, Eitze S, Korn L, Goldhahn L, Schmitz JM, Giesler P, Knauer G, Jenny MA. Empirical evidence to understand the human factor for effective rapid testing against SARS-CoV-2. Proc Natl Acad Sci U S A 2021; 118:e2107179118. [PMID: 34362848 PMCID: PMC8364214 DOI: 10.1073/pnas.2107179118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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] [Indexed: 11/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapid antigen point-of-care and home tests are available to laypeople. In four cross-sectional mixed-methods data collections conducted between December 2020 and March 2021 (n = 4,026), we showed that a majority of subjects were willing to test despite mistrust and ignorance regarding rapid tests' validity. Experimental evidence shows that low costs and access to events could increase testing intentions. Mandatory reporting and isolation after positive results were not identified as major barriers. Instead, assuming that testing and isolation can slow down the pandemic and the possibility to protect others were related to greater willingness to get tested. While we did not find evidence for risk compensation for past tests, experimental evidence suggests that there is a tendency to show less mask wearing and physical distancing in a group of tested individuals. A short communication intervention reduced complacent behavior. The derived recommendations could make rapid testing a successful pillar of pandemic management.
Collapse
Affiliation(s)
- Cornelia Betsch
- Center for Empirical Research in Economics and Behavioral Sciences, University of Erfurt, 99089 Erfurt, Germany;
- Communication Science, University of Erfurt, 99089 Erfurt, Germany
| | - Philipp Sprengholz
- Center for Empirical Research in Economics and Behavioral Sciences, University of Erfurt, 99089 Erfurt, Germany
- Communication Science, University of Erfurt, 99089 Erfurt, Germany
| | - Regina Siegers
- Communication Science, University of Erfurt, 99089 Erfurt, Germany
| | - Sarah Eitze
- Center for Empirical Research in Economics and Behavioral Sciences, University of Erfurt, 99089 Erfurt, Germany
- Communication Science, University of Erfurt, 99089 Erfurt, Germany
| | - Lars Korn
- Center for Empirical Research in Economics and Behavioral Sciences, University of Erfurt, 99089 Erfurt, Germany
- Communication Science, University of Erfurt, 99089 Erfurt, Germany
| | - Laura Goldhahn
- Communication Science, University of Erfurt, 99089 Erfurt, Germany
| | | | - Paula Giesler
- Communication Science, University of Erfurt, 99089 Erfurt, Germany
| | - Gesine Knauer
- Communication Science, University of Erfurt, 99089 Erfurt, Germany
| | - Mirjam A Jenny
- Science Communication Unit, Robert Koch Institute, 13353 Berlin, Germany
- Center for Adaptive Rationality, Max Planck Institute for Human Development, 14195 Berlin, Germany
- Harding Center for Risk Literacy, University of Potsdam, 14482 Potsdam, Germany
| |
Collapse
|
30
|
Kolesnik-Goldmann N, Bodendoerfer E, Röthlin K, Herren S, Imkamp F, Marchesi M, Mancini S. Rapid Detection of PBP2a in Staphylococci from Shortly Incubated Subcultures of Positive Blood Cultures by an Immunochromatographic Assay. Microbiol Spectr 2021;:e0046221. [PMID: 34319135 DOI: 10.1128/Spectrum.00462-21] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus, as well as coagulase-negative staphylococci (CoNS), can cause a wide range of human infections both in nosocomial and community settings. Βeta-lactams are the antibiotics of choice for the treatment of bloodstream infections (BSI) caused by these microorganisms. Resistance to virtually all β-lactams (also referred to as methicillin resistance) primarily results from the production of an alternative penicillin-binding protein (PBP2a) encoded by the mecA gene. While β-lactams are still used as first-line therapy against BSI caused by S. aureus, BSI with CoNS are usually treated with vancomycin due to the high prevalence of methicillin resistance. Rapid detection of methicillin resistance is thus critical for continuation or adjustment of the empirical therapy and therewith to improve the clinical outcome of the patients. The revised version of the immunochromatographic assay PBP2a SA culture colony test (SACCT) is a rapid, inexpensive, and easy method that enables reliable detection of PBP2a in mecA-positive staphylococcal isolates after18 to 24 h of incubation. Here, we evaluated the diagnostic performance of the SACCT using primary subcultures of spiked blood cultures after short incubation (4 to 6 h) and established a modified procedure with an equal analytical performance to that of longer-grown cultures. With the proposed method the SACCT can be employed for PBP2a detection from shortly incubated subcultures of clinically relevant staphylococcal isolates, thereby allowing more rapid and effective management of BSI caused by these organisms. IMPORTANCE Antibiotic resistance poses a major threat to health and incurs high economic costs worldwide. Rapid detection of resistance mechanisms can contribute to improving patient care and preventing the dissemination of antimicrobial resistance. Here, we describe a rapid method to detect the most important beta-lactam resistance mechanism (the plasmid-encoded alternative transpeptidase PBP2a) in staphylococcal isolates causing BSI. We show that, using a modified procedure, PBP2a can be reliably detected from primary subcultures of spiked blood cultures after short incubation (4 to 6 h) with a rapid, inexpensive, and simple immunochromatographic test (SACCT). We provide an accurate, inexpensive, and rapid method to facilitate appropriate management and control of infections in patients suffering from invasive staphylococcal infections.
Collapse
|
31
|
Berinson B, Both A, Berneking L, Christner M, Lütgehetmann M, Aepfelbacher M, Rohde H. Usefulness of BioFire FilmArray BCID2 for Blood Culture Processing in Clinical Practice. J Clin Microbiol 2021; 59:e0054321. [PMID: 33980648 DOI: 10.1128/JCM.00543-21] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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] [Indexed: 12/11/2022] Open
Abstract
Rapid pathogen characterization from positive blood cultures (BC) can improve management of patients with bloodstream infections (BSI). The FilmArray blood culture identification (BCID) assay is a molecular test approved for direct identification of BSI causing pathogens from positive BC. A recently updated version of the panel (BCID2) comprises improved species identification characteristics and allows for the detection of one expanded-spectrum β-lactamase (ESBL)- and several carbapenemase-encoding genes. Here, the clinical performance of the BCID2 assay for species identification in 180 positive BCs was evaluated. BCID2 results were concordant with the standard of care (SOC) in 159/180 (88.3%) BCs; 68/74 (91.9%) and 71/74 (96.0%) of all samples growing monobacterial, Gram-positive or Gram-negative pathogens, respectively, were identified, in agreement with SOC results. Nonconcordance was related to the detection of additional pathogens by the BCID2 assay (n = 4), discrepant species identification (n = 4), or failure of BCID2 to detect on-panel pathogens (n = 1). A number (12/31; 38.7%) of discordant results became evident in polymicrobial BC specimens. BCID2 identified the presence of blaCTX-M-carrying species in 12 BC specimens but failed to predict third-generation cephalosporin resistance in four isolates exhibiting independent cephalosporin resistance mechanisms. Carbapenem resistance related to the presence of blaVIM-2 or blaOxa-48-like was correctly predicted in two isolates. In conclusion, the BCID2 assay is a reliable tool for rapid BC processing and species identification. Despite inclusion of common ESBL- or carbapenemase-encoding markers, the multifactorial nature of β-lactam resistance in Gram-negative organisms warrants combination of BCID2 with (rapid) phenotypic susceptibility assays.
Collapse
|
32
|
Mahmoud SA, Ganesan S, Ibrahim E, Thakre B, Teddy JG, Raheja P, Zaher WA. Evaluation of six different rapid methods for nucleic acid detection of SARS-COV-2 virus. J Med Virol 2021; 93:5538-5543. [PMID: 34002401 PMCID: PMC8242416 DOI: 10.1002/jmv.27090] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 03/31/2021] [Revised: 05/05/2021] [Accepted: 05/13/2021] [Indexed: 01/30/2023]
Abstract
In the current coronavirus disease 2019 (COVID‐19) pandemic there is a mass screening of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) happening around the world due to the extensive spread of the infections. There is a high demand for rapid diagnostic tests to expedite the identification of cases and to facilitate early isolation and control spread. Hence this study evaluates six different rapid nucleic acid detection assays that are commercially available for SARS‐CoV‐2 virus detection. Nasopharyngeal samples were collected from 4981 participants and were tested for the SARS‐CoV‐2 virus by the gold standard real‐time reverse‐transcription polymerase chain reaction (RT‐PCR) method and with one of these six rapid methods of detection. Evaluation of the rapid nucleic acid detection assays was done by comparing the results of these rapid methods with the gold standard RT‐qPCR results for SARS‐COV‐2 detection. AQ‐TOP had the highest sensitivity (98%) and a strong kappa value of 0.943 followed by Genechecker and Abbot ID NOW. The POCKIT (ii RT‐PCR) assay had the highest test accuracy of 99.29% followed by Genechecker and Cobas Liat. Atila iAMP showed the highest percentage of invalid reports (35.5%) followed by AQ‐TOP with 6% and POCKIT with 3.7% of invalid reports. Genechecker system, Abbott ID NOW, and Cobas Liat were found to have the best performance and agreement when compared with the standard RT‐PCR for COVID‐19 detection. With further research, these rapid tests have the potential to be employed in large‐scale screening of COVID‐19. The rapid nucleic acid detection kits for detection of SARS‐COV‐2, has the potential to be employed as mass testing strategy. Variable sensitivity and specificity have been identified for the different rapid detection platforms. This evaluation will help laboratories in making choices on purchasing and further evaluation of these platforms. This evaluation considers various parameters like the diagnostic reliability of the platforms, turn around time and throughput, which are not much evaluated in other papers.
Collapse
|
33
|
Hijos-Mallada G, Lué A, Velamazan R, Saura N, Abril C, Lorenzo M, Navarro M, Chueca E, Arechavaleta S, Gomollón F, Lanas Á, Sostres C. The Addition of Other Fecal Biomarkers Does Not Improve the Diagnostic Accuracy of Immunochemical Fecal Occult Blood Test Alone in a Colorrectal Cancer Screening Cohort. Front Med (Lausanne) 2021; 8:665786. [PMID: 34150803 PMCID: PMC8212973 DOI: 10.3389/fmed.2021.665786] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/11/2021] [Indexed: 01/13/2023] Open
Abstract
Background: Screening with fecal occult blood test reduces colorectal cancer (CRC) incidence and mortality, and is currently implemented in most countries. However, around 40% of screening colonoscopies are normal. Thus, strategies to avoid these colonoscopies are highly necessary. Adding other fecal biomarkers, such as fecal calprotectin (FC), lactoferrin, and transferrin may be useful, but evidence is scarce. Aims: To evaluate the diagnostic accuracy of fecal occult blood immunochemical test (FIT), FC, and a one-step combo card test for the simultaneous semi-qualitative detection of human hemoglobin (hHb), transferrin (hTf), calprotectin (hCp) and lactoferrin (hLf) in a CRC screening program population. Methods: Single-center, prospective observational study, enrolling patients included in a CRC screening program, referred for a colonoscopy due to a positive FIT test. Participants collected a stool sample prior to bowel preparation, and FIT, FC and the combo semi-qualitative tests were performed on the sample. Sensitivity, specificity, positive and negative predictive values and area under receiver operator curve (AUC) for diagnosis of advanced neoplasia, advanced adenoma and CRC were estimated for each biomarker and their combinations. The primary endpoint of the study was to assess whether these biomarkers could improve the diagnostic accuracy of FIT alone. Results: 336 consecutive patients (64% males) were recruited. Advanced neoplasia was found in 129/336 (38.4%) patients, and of these, 22/336 (6.5%) were diagnosed of CRC. 153/336 (45.5%) colonoscopies were completely normal. The AUC for the diagnosis of advanced neoplasia were 0.725 (95%CI 0.665–0.784) for FIT, 0.477 (95%CI 0.413–0.541) for FC and 0.732 (95%CI 0.674–0.791) for the combination of both (FIT + FC) quantitative tests. The AUCs for the combo test were 0.70 (95%CI 0.641–0.760) for hHb, 0.625 (95%CI 0.562–0.698) for hTf, 0.532 (95%CI 0.469–0.595) for hCp, 0.531 (95%CI 0.466–0.595 ) for hLf and 0.681 (95%CI 0.620–0.741) for the combination of the four biomarkers. Conclusion: In average-risk population, FIT appears to be the best fecal marker for the diagnosis of CRC and advanced adenoma. None of the other biomarkers explored or their combinations provided a better diagnostic accuracy. Only hTF showed an acceptable diagnostic accuracy. FC and hLF were not useful in this setting.
Collapse
Affiliation(s)
- Gonzalo Hijos-Mallada
- Digestive Diseases Service, University Clinic Hospital, Zaragoza, Spain.,Aragón Health Research Institute (IIS Aragón), Zaragoza, Spain
| | - Alberto Lué
- Digestive Diseases Service, University Clinic Hospital, Zaragoza, Spain.,Aragón Health Research Institute (IIS Aragón), Zaragoza, Spain
| | - Raul Velamazan
- Digestive Diseases Service, University Clinic Hospital, Zaragoza, Spain.,Aragón Health Research Institute (IIS Aragón), Zaragoza, Spain
| | - Nuria Saura
- Digestive Diseases Service, University Clinic Hospital, Zaragoza, Spain.,Aragón Health Research Institute (IIS Aragón), Zaragoza, Spain
| | | | | | - Mercedes Navarro
- Digestive Diseases Service, University Clinic Hospital, Zaragoza, Spain.,Aragón Health Research Institute (IIS Aragón), Zaragoza, Spain
| | - Eduardo Chueca
- Aragón Health Research Institute (IIS Aragón), Zaragoza, Spain.,CIBER Enfermedades Hepáticas y Digestivas (CIBERehd), Zaragoza, Spain
| | - Samantha Arechavaleta
- Aragón Health Research Institute (IIS Aragón), Zaragoza, Spain.,CIBER Enfermedades Hepáticas y Digestivas (CIBERehd), Zaragoza, Spain
| | - Fernando Gomollón
- Digestive Diseases Service, University Clinic Hospital, Zaragoza, Spain.,Aragón Health Research Institute (IIS Aragón), Zaragoza, Spain.,University of Zaragoza, Zaragoza, Spain.,CIBER Enfermedades Hepáticas y Digestivas (CIBERehd), Zaragoza, Spain
| | - Ángel Lanas
- Digestive Diseases Service, University Clinic Hospital, Zaragoza, Spain.,Aragón Health Research Institute (IIS Aragón), Zaragoza, Spain.,University of Zaragoza, Zaragoza, Spain.,CIBER Enfermedades Hepáticas y Digestivas (CIBERehd), Zaragoza, Spain
| | - Carlos Sostres
- Digestive Diseases Service, University Clinic Hospital, Zaragoza, Spain.,Aragón Health Research Institute (IIS Aragón), Zaragoza, Spain.,University of Zaragoza, Zaragoza, Spain.,CIBER Enfermedades Hepáticas y Digestivas (CIBERehd), Zaragoza, Spain
| |
Collapse
|
34
|
Cerino P, Gallo A, Pierri B, Buonerba C, Di Concilio D, Cuomo MC, Vassallo L, Lo Conte G, Coppola A, Pizzolante A, Boccia G, Ferrucci V, Atripaldi L, Triassi M, Pacella D, Cennamo M, Romano P, Sorbo TM, Furno A, Catapano O, Contina A, Perruolo G, D'Amora M, Terracciano D, Portella G. Seroprevalence of SARS-CoV-2 Assessed by Four Chemiluminescence Immunoassays and One Immunocromatography Test for SARS-Cov-2. Front Public Health 2021; 9:649781. [PMID: 33996728 PMCID: PMC8116632 DOI: 10.3389/fpubh.2021.649781] [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: 01/05/2021] [Accepted: 03/05/2021] [Indexed: 12/30/2022] Open
Abstract
The onset of the new SARS-CoV-2 coronavirus encouraged the development of new serologic tests that could be additional and complementary to real-time RT-PCR-based assays. In such a context, the study of performances of available tests is urgently needed, as their use has just been initiated for seroprevalence assessment. The aim of this study was to compare four chemiluminescence immunoassays and one immunochromatography test for SARS-Cov-2 antibodies for the evaluation of the degree of diffusion of SARS-CoV-2 infection in Salerno Province (Campania Region, Italy). A total of 3,185 specimens from citizens were tested for anti-SARS-CoV-2 antibodies as part of a screening program. Four automated immunoassays (Abbott and Liaison SARS-CoV-2 CLIA IgG and Roche and Siemens SARS-CoV-2 CLIA IgM/IgG/IgA assays) and one lateral flow immunoassay (LFIA Technogenetics IgG–IgM COVID-19) were used. Seroprevalence in the entire cohort was 2.41, 2.10, 1.82, and 1.85% according to the Liaison IgG, Abbott IgG, Siemens, and Roche total Ig tests, respectively. When we explored the agreement among the rapid tests and the serologic assays, we reported good agreement for Abbott, Siemens, and Roche (Cohen's Kappa coefficient 0.69, 0.67, and 0.67, respectively), whereas we found moderate agreement for Liaison (Cohen's kappa coefficient 0.58). Our study showed that Abbott and Liaison SARS-CoV-2 CLIA IgG, Roche and Siemens SARS-CoV-2 CLIA IgM/IgG/IgA assays, and LFIA Technogenetics IgG-IgM COVID-19 have good agreement in seroprevalence assessment. In addition, our findings indicate that the prevalence of IgG and total Ig antibodies against SARS-CoV-2 at the time of the study was as low as around 3%, likely explaining the amplitude of the current second wave.
Collapse
Affiliation(s)
- Pellegrino Cerino
- Centro di Referenza Nazionale per l'Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Alfonso Gallo
- Centro di Referenza Nazionale per l'Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Biancamaria Pierri
- Centro di Referenza Nazionale per l'Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy.,Department of Medicine, Surgery, and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy
| | - Carlo Buonerba
- Centro di Referenza Nazionale per l'Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy.,Regional Reference Center for Rare Tumors, Department of Oncology and Hematology, Azienda Ospedaliera Universitaria Federico II of Naples, Naples, Italy
| | - Denise Di Concilio
- Centro di Referenza Nazionale per l'Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Maria Concetta Cuomo
- Centro di Referenza Nazionale per l'Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Lucia Vassallo
- Centro di Referenza Nazionale per l'Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Gabriella Lo Conte
- Centro di Referenza Nazionale per l'Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Annachiara Coppola
- Centro di Referenza Nazionale per l'Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Antonio Pizzolante
- Centro di Referenza Nazionale per l'Analisi e Studio di Correlazione tra Ambiente, Animale e Uomo, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Giovanni Boccia
- Department of Medicine, Surgery, and Dentistry 'Scuola Medica Salernitana', University of Salerno, Baronissi, Italy
| | | | - Luigi Atripaldi
- Cotugno Hospital, Azienda Ospedaliera di Rilievo Nazionale Ospedali dei Colli, Naples, Italy
| | - Maria Triassi
- Department of Public Health, Section of Hygiene, University of Naples Federico II, Naples, Italy
| | - Daniela Pacella
- Department of Public Health, Section of Hygiene, University of Naples Federico II, Naples, Italy
| | - Michele Cennamo
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Paolo Romano
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Teresa Maria Sorbo
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Alessandro Furno
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Oriana Catapano
- Unità Operativa Complessa Medicina di laboratorio P. O. San Paolo, Azienda Sanitaria Locale Naples 1 Centro, Naples, Italy
| | - Aldo Contina
- Unità Operativa Complessa Medicina di laboratorio P. O. San Paolo, Azienda Sanitaria Locale Naples 1 Centro, Naples, Italy
| | - Giuseppe Perruolo
- Unità Operativa Complessa Medicina di laboratorio P. O. San Paolo, Azienda Sanitaria Locale Naples 1 Centro, Naples, Italy
| | - Maurizio D'Amora
- Unità Operativa Complessa Medicina di laboratorio P. O. San Paolo, Azienda Sanitaria Locale Naples 1 Centro, Naples, Italy
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Giuseppe Portella
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| |
Collapse
|
35
|
Chapot V, Effenberg L, Dohmen-Ruetten J, Buer J, Kehrmann J. Evaluation of the Accelerate Pheno System for Rapid Identification and Antimicrobial Susceptibility Testing of Positive Blood Culture Bottles Inoculated with Primary Sterile Specimens from Patients with Suspected Severe Infections. J Clin Microbiol 2021; 59:e02637-20. [PMID: 33568464 DOI: 10.1128/JCM.02637-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/05/2021] [Indexed: 01/25/2023] Open
Abstract
The Accelerate Pheno system is approved for rapid identification and phenotypic antimicrobial susceptibility testing (AST) of microorganisms grown from positive blood cultures inoculated with blood from septic patients. We evaluated the performance of the system for identification and AST from positive blood culture bottles inoculated with primary sterile nonblood specimens from patients with suspected severe infections. One hundred positive blood culture bottles with primary sterile specimens (63 cerebrospinal fluids, 16 ascites, 7 pleural fluids, 4 vitreous fluids, 5 joint aspirates, and 5 other aspirates) from 100 patients were included. Pathogen identification was in agreement with conventional methods for 72 of 100 cultures (72%) and for 81 of 112 (72%) pathogens when considering all pathogens and for 72 of 92 (78%) cultures and 81 of 104 (78%) pathogens when considering on-panel pathogens only. Eight of 31 isolates (26%) not identified by APS were pathogens not included in the APS panel. APS and conventional methods accordingly identified all pathogens from two of nine polymicrobial cultures (22%). APS generated antimicrobial resistance results for 57 pathogens of 57 cultures. The overall category agreement between APS and culture-based AST was 91.2%; and the rate for minor errors was 6.9%, for major was 1.7%, and for very major errors was 0.2%. APS may accelerate pathogen identification and phenotypic AST from positive blood culture bottles inoculated with primary sterile specimens from patients with serious infections, especially for hospitals without an on-site microbiology laboratory. However, the inclusion of nonblood specimens with a high likelihood of polymicrobial infections may result in an inferior performance.
Collapse
|
36
|
Södersten E, Ongarello S, Mantsoki A, Wyss R, Persing DH, Banderby S, Strömqvist Meuzelaar L, Prieto J, Gnanashanmugam D, Khatri P, Schumacher SG, Denkinger CM. Diagnostic Accuracy Study of a Novel Blood-Based Assay for Identification of Tuberculosis in People Living with HIV. J Clin Microbiol 2021; 59:e01643-20. [PMID: 33298607 DOI: 10.1128/JCM.01643-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 07/03/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022] Open
Abstract
A nonsputum triage test to rule out tuberculosis (TB) disease is a WHO high-priority diagnostic, and a combinatory score based on a 3-gene host signature has shown promise in discriminating TB from other illnesses. We evaluated the accuracy of an early-prototype cartridge assay (“Xpert MTB Host Response” or Xpert-MTB-HR-Prototype) of this 3-gene signature on biobanked blood samples from people living with HIV (PLHIV) against a comprehensive microbiological reference standard (CMRS) and against Xpert MTB/RIF on the first sputum sample alone. A nonsputum triage test to rule out tuberculosis (TB) disease is a WHO high-priority diagnostic, and a combinatory score based on a 3-gene host signature has shown promise in discriminating TB from other illnesses. We evaluated the accuracy of an early-prototype cartridge assay (“Xpert MTB Host Response” or Xpert-MTB-HR-Prototype) of this 3-gene signature on biobanked blood samples from people living with HIV (PLHIV) against a comprehensive microbiological reference standard (CMRS) and against Xpert MTB/RIF on the first sputum sample alone. We depict results based on performance targets set by the WHO in comparison with a laboratory-based C-reactive protein (CRP) assay. Of 201 patients included, 67 were culture positive for Mycobacterium tuberculosis. The areas under the concentration-time curve (AUCs) for Xpert-MTB-HR-Prototype were 0.89 (confidence interval [CI], 0.83 to 0.94) against the CMRS and 0.94 (CI, 0.89 to 0.98) against Xpert MTB/RIF. Considering Xpert-MTB-HR-Prototype as a triage test (at the nearest upper value of sensitivity to 90%), specificities were 55.8% (CI, 47.2 to 64.1%) compared to the CMRS and 85.9% (CI, 79.3 to 90.7%) compared to Xpert MTB/RIF as confirmatory tests. Considering Xpert-MTB-HR-Prototype as a stand-alone diagnostic test, at a specificity near 95%, the test achieved a sensitivity of 65.7% (CI, 53.7 to 75.9%), while the CRP assay achieved a sensitivity of only 13.6% (CI, 7.3 to 23.4%). In this first accuracy study of a prototype blood-based host marker assay, we show the possible value of the assay for triage and diagnosis in PLHIV.
Collapse
|
37
|
Anahtar MN, McGrath GEG, Rabe BA, Tanner NA, White BA, Lennerz JKM, Branda JA, Cepko CL, Rosenberg ES. Clinical Assessment and Validation of a Rapid and Sensitive SARS-CoV-2 Test Using Reverse Transcription Loop-Mediated Isothermal Amplification Without the Need for RNA Extraction. Open Forum Infect Dis 2021; 8:ofaa631. [PMID: 34853795 PMCID: PMC7798487 DOI: 10.1093/ofid/ofaa631] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/15/2020] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Amid the enduring pandemic, there is an urgent need for expanded access to rapid, sensitive, and inexpensive coronavirus disease 2019 (COVID-19) testing worldwide without specialized equipment. We developed a simple test that uses colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) to detect severe acute resrpiratory syndrome coronavirus 2 (SARS-CoV-2) in 40 minutes from sample collection to result. METHODS We tested 135 nasopharyngeal specimens from patients evaluated for COVID-19 infection at Massachusetts General Hospital. Specimens were either added directly to RT-LAMP reactions, inactivated by a combined chemical and heat treatment step, or inactivated then purified with a silica particle-based concentration method. Amplification was performed with 2 SARS-CoV-2-specific primer sets and an internal specimen control; the resulting color change was visually interpreted. RESULTS Direct RT-LAMP testing of unprocessed specimens could only reliably detect samples with abundant SARS-CoV-2 (>3 000 000 copies/mL), with sensitivities of 50% (95% CI, 28%-72%) and 59% (95% CI, 43%-73%) in samples collected in universal transport medium and saline, respectively, compared with quantitative polymerase chain reaction (qPCR). Adding an upfront RNase inactivation step markedly improved the limit of detection to at least 25 000 copies/mL, with 87.5% (95% CI, 72%-95%) sensitivity and 100% specificity (95% CI, 87%-100%). Using both inactivation and purification increased the assay sensitivity by 10-fold, achieving a limit of detection comparable to commercial real-time PCR-based diagnostics. CONCLUSIONS By incorporating a fast and inexpensive sample preparation step, RT-LAMP accurately detects SARS-CoV-2 with limited equipment for about US$6 per sample, making this a potentially ideal assay to increase testing capacity, especially in resource-limited settings.
Collapse
Affiliation(s)
- Melis N Anahtar
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Graham E G McGrath
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Brian A Rabe
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Ophthalmology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Benjamin A White
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jochen K M Lennerz
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - John A Branda
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Constance L Cepko
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Ophthalmology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Eric S Rosenberg
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| |
Collapse
|
38
|
Majdinasab M, Ben Aissa S, Marty JL. Advances in Colorimetric Strategies for Mycotoxins Detection: Toward Rapid Industrial Monitoring. Toxins (Basel) 2020; 13:13. [PMID: 33374434 PMCID: PMC7823678 DOI: 10.3390/toxins13010013] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 11/30/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
Mycotoxins contamination is a global public health concern. Therefore, highly sensitive and selective techniques are needed for their on-site monitoring. Several approaches are conceivable for mycotoxins analysis, among which colorimetric methods are the most attractive for commercialization purposes thanks to their visual read-out, easy operation, cost-effectiveness, and rapid response. This review covers the latest achievements in the last five years for the development of colorimetric methods specific to mycotoxins analysis, with a particular emphasis on their potential for large-scale applications in food industries. Gathering all types of (bio)receptors, main colorimetric methods are critically discussed, including enzyme-linked assays, lateral flow-assays, microfluidic devices, and homogenous in-solution strategies. This special focus on colorimetry as a versatile transduction method for mycotoxins analysis is comprehensively reviewed for the first time.
Collapse
Affiliation(s)
- Marjan Majdinasab
- Department of Food Science & Technology, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran;
| | - Sondes Ben Aissa
- BAE-LBBM Laboratory, University of Perpignan via Domitia, 52 Avenue Paul Alduy, CEDEX 9, 66860 Perpignan, France;
| | - Jean Louis Marty
- BAE-LBBM Laboratory, University of Perpignan via Domitia, 52 Avenue Paul Alduy, CEDEX 9, 66860 Perpignan, France;
| |
Collapse
|
39
|
Lopez-Albizu C, Danesi E, Piorno P, Fernandez M, García Campos F, Scollo K, Crudo F. Rapid Diagnostic Tests for Trypanosoma cruzi Infection: Field Evaluation of Two Registered Kits in a Region of Endemicity and a Region of Nonendemicity in Argentina. J Clin Microbiol 2020; 58:e01140-20. [PMID: 32938737 DOI: 10.1128/JCM.01140-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 05/25/2020] [Accepted: 07/22/2020] [Indexed: 01/04/2023] Open
Abstract
Infection by Trypanosoma cruzi (Chagas disease [ChD]) affects around 7 million people in the Americas, most of whom are unaware of their status due to lack of clinical manifestations and poor access to diagnosis. Rapid diagnostic tests (RDTs) are widely used for screening for different infections (HIV, hepatitis B, and syphilis), and their application for ChD would facilitate access to diagnosis, especially in remote areas where health services have scarce resources. We conducted a prospective intervention study in 2018 to evaluate in the field two in vitro RDTs for ChD, authorized by the National Administration of Medicaments, Aliments, and Medical Technologies of Argentina (ANMAT), in areas of endemicity and nonendemicity in Argentina. Infection by Trypanosoma cruzi (Chagas disease [ChD]) affects around 7 million people in the Americas, most of whom are unaware of their status due to lack of clinical manifestations and poor access to diagnosis. Rapid diagnostic tests (RDTs) are widely used for screening for different infections (HIV, hepatitis B, and syphilis), and their application for ChD would facilitate access to diagnosis, especially in remote areas where health services have scarce resources. We conducted a prospective intervention study in 2018 to evaluate in the field two in vitro RDTs for ChD, authorized by the National Administration of Medicaments, Aliments, and Medical Technologies of Argentina (ANMAT), in areas of endemicity and nonendemicity in Argentina. We recruited 607 volunteers older than 18 years in Salta province and the city of Buenos Aires. The RDTs Ab Standard Diagnostics SD Bioline (SD) and Check Chagas Wiener Lab (WL) were performed in situ with whole-blood samples, and confirmatory serology was done at a reference center. The rate of infection with T. cruzi was 17.8% (108/607). The SD test showed 97.2% sensitivity (95% confidence interval [CI], 93.5 to 100) and 91.7% specificity (95% CI, 96.2 to 99.2%), and the WL test showed 93.4% sensitivity (95% CI, 88.2 to 98.6%) and 99.1% specificity (95% CI, 91.9 to 100%). The sensitivity and specificity for the two RDTs tested were higher than previously reported. These results encourage the use of the tested RDTs in Salta province and for further field studies for the implementation of these RDTs in other epidemiological scenarios. This will be very important to improve access to diagnosis of Chagas and its clinical management as a neglected disease, especially in remote areas with health access barriers.
Collapse
|
40
|
Abstract
Pour faire face à l’émergence du Sars-CoV-2 responsable d’une pandémie mondiale, de très nombreux tests diagnostiques ont été développés et mis sur le marché dans un délai très court. La RT-PCR sur prélèvement rhino-pharyngé est la méthode de référence pour le diagnostic et le dépistage de l’infection à Sars-CoV-2 mais les tests développés présentent de grande variabilité en termes de sensibilité et de délai de rendu des résultats. Les tests antigéniques présentent en général une sensibilité plus faible mais présentent l’avantage d’une mise en œuvre plus simple et plus rapide. Devant des tableaux évoca-teurs de Covid-19 avec un résultat de RT-PCR négatif, une sérologie peut être recommandée avec le dosage des IgM et des IgG. La sérologie est également un outil pertinent pour les études épidémiologiques. Néanmoins il est important de rappeler que le taux d’anticorps anti-Sars-Cov-2 décroit avec le temps et peut ainsi impacter les résultats d’études séro-épidémiologiques. Malgré la nécessité de répondre rapidement à un besoin diagnostique urgent, il demeure indispensable de valider les méthodes choisies sur un panel d’échantillons bien caractérisé, les performances de certains tests étant parfois insatisfaisantes pour assurer un diagnostic fiable.
Collapse
Affiliation(s)
- Sébastien Hantz
- Laboratoire de bactériologie-virologie-hygiène, Centre de biologie et de recherche en santé François-Denis, CHU Limoges, rue Bernard-Descottes, 87000 Limoges, France
| |
Collapse
|
41
|
Buonomini AR, Riva E, Di Bonaventura G, Gherardi G. Rapid Detection of Methicillin-Resistant Staphylococcus aureus Directly from Blood for the Diagnosis of Bloodstream Infections: A Mini-Review. Diagnostics (Basel) 2020; 10:E830. [PMID: 33076535 DOI: 10.3390/diagnostics10100830] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/22/2020] [Accepted: 10/14/2020] [Indexed: 11/23/2022] Open
Abstract
Staphylococcus aureus represents a major human pathogen able to cause a number of infections, especially bloodstream infections (BSI). Clinical use of methicillin has led to the emergence of methicillin-resistant S. aureus (MRSA) and MRSA-BSI have been reported to be associated with high morbidity and mortality. Clinical diagnosis of BSI is based on the results from blood culture that, although considered the gold standard method, is time-consuming. For this reason, rapid diagnostic tests to identify the presence of methicillin-susceptible S. aureus (MSSA) and MRSA isolates directly in blood cultures are being used with increasing frequency to rapidly commence targeted antimicrobial therapy, also in the light of antimicrobial stewardship efforts. Here, we review and report the most common rapid non-molecular and molecular methods currently available to detect the presence of MRSA directly from blood.
Collapse
|
42
|
Pavlova IP, Nair SS, Kyprianou N, Tewari AK. The Rapid Coronavirus Antibody Test: Can We Improve Accuracy? Front Med (Lausanne) 2020; 7:569. [PMID: 32984390 PMCID: PMC7492556 DOI: 10.3389/fmed.2020.00569] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/11/2020] [Indexed: 01/21/2023] Open
Affiliation(s)
- Ina P. Pavlova
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Sujit S. Nair
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Natasha Kyprianou
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ash K. Tewari
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| |
Collapse
|
43
|
Visseaux B, Le Hingrat Q, Collin G, Bouzid D, Lebourgeois S, Le Pluart D, Deconinck L, Lescure FX, Lucet JC, Bouadma L, Timsit JF, Descamps D, Yazdanpanah Y, Casalino E, Houhou-Fidouh N. Evaluation of the QIAstat-Dx Respiratory SARS-CoV-2 Panel, the First Rapid Multiplex PCR Commercial Assay for SARS-CoV-2 Detection. J Clin Microbiol 2020; 58:e00630-20. [PMID: 32341142 PMCID: PMC7383528 DOI: 10.1128/jcm.00630-20] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [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: 04/01/2020] [Accepted: 04/23/2020] [Indexed: 01/22/2023] Open
Abstract
In the race to contain severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), efficient detection and triage of infected patients must rely on rapid and reliable testing. In this work, we performed the first evaluation of the QIAstat-Dx respiratory SARS-CoV-2 panel (QIAstat-SARS) for SARS-CoV-2 detection. This assay is the first rapid multiplex PCR (mPCR) assay, including SARS-CoV-2 detection, and is fully compatible with a non-PCR-trained laboratory or point-of-care (PoC) testing. This evaluation was performed using 69 primary clinical samples (66 nasopharyngeal swabs [NPS], 1 bronchoalveolar lavage fluid sample [BAL], 1 tracheal aspirate sample, and 1 bronchial aspirate sample) comparing SARS-CoV-2 detection with the currently WHO-recommended reverse transcription-PCR (RT-PCR) (WHO-RT-PCR) workflow. Additionally, a comparative limit of detection (LoD) assessment was performed for QIAstat-SARS and WHO-RT-PCR using a quantified clinical sample. Compatibility of sample pretreatment for viral neutralization or viscous samples with the QIAstat-SARS system were also tested. The QIAstat-Dx respiratory SARS-CoV-2 panel demonstrated a sensitivity comparable to that of the WHO-recommended assay with a limit of detection at 1,000 copies/ml. The overall percent agreement between QIAstat-Dx SARS and WHO-RT-PCR on 69 clinical samples was 97% with a sensitivity of 100% (40/40) and specificity at 93% (27/29). No cross-reaction was encountered for any other respiratory viruses or bacteria included in the panel. The QIAstat-SARS rapid multiplex PCR panel provides a highly sensitive, robust, and accurate assay for rapid detection of SARS-CoV-2. This assay allows rapid decisions even in non-PCR-trained laboratory or point-of-care testing, allowing innovative organization.
Collapse
Affiliation(s)
- Benoit Visseaux
- Université de Paris, Assistance Publique - Hôpitaux de Paris, Service de Virologie, Hôpital Bichat, Paris, France
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France
| | - Quentin Le Hingrat
- Université de Paris, Assistance Publique - Hôpitaux de Paris, Service de Virologie, Hôpital Bichat, Paris, France
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France
| | - Gilles Collin
- Université de Paris, Assistance Publique - Hôpitaux de Paris, Service de Virologie, Hôpital Bichat, Paris, France
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France
| | - Donia Bouzid
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France
- Université de Paris, Assistance Publique - Hôpitaux de Paris, Service d'Accueil des Urgences, Hôpital Bichat, Paris, France
| | - Samuel Lebourgeois
- Université de Paris, Assistance Publique - Hôpitaux de Paris, Service de Virologie, Hôpital Bichat, Paris, France
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France
| | - Diane Le Pluart
- Université de Paris, Service de Maladies Infectieuses et Tropicales, Hôpital Bichat Claude Bernard, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Laurène Deconinck
- Université de Paris, Service de Maladies Infectieuses et Tropicales, Hôpital Bichat Claude Bernard, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - François-Xavier Lescure
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France
- Université de Paris, Service de Maladies Infectieuses et Tropicales, Hôpital Bichat Claude Bernard, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Jean-Christophe Lucet
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France
- Université de Paris, Unité d'Hygiène et de Lutte contre les Infections Nosocomiales, Hôpital Bichat Claude Bernard, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Lila Bouadma
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France
- Université de Paris, Réanimation Médicale et Infectieuse, Hôpital Bichat Claude Bernard, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Jean-François Timsit
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France
- Université de Paris, Réanimation Médicale et Infectieuse, Hôpital Bichat Claude Bernard, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Diane Descamps
- Université de Paris, Assistance Publique - Hôpitaux de Paris, Service de Virologie, Hôpital Bichat, Paris, France
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France
| | - Yazdan Yazdanpanah
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France
- Université de Paris, Service de Maladies Infectieuses et Tropicales, Hôpital Bichat Claude Bernard, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Enrique Casalino
- UMR 1137-IAME, Decision Sciences in Infectious Diseases Control and Care (DeSCID), INSERM, Université de Paris, Paris, France
- Université de Paris, Assistance Publique - Hôpitaux de Paris, Service d'Accueil des Urgences, Hôpital Bichat, Paris, France
| | | |
Collapse
|
44
|
Tollånes MC, Bakken Kran AM, Abildsnes E, Jenum PA, Breivik AC, Sandberg S. Evaluation of eleven rapid tests for detection of antibodies against SARS-CoV-2. Clin Chem Lab Med 2020; 58:1595-1600. [PMID: 32598303 DOI: 10.1515/cclm-2020-0628] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 04/30/2020] [Accepted: 05/29/2020] [Indexed: 12/29/2022]
Abstract
Objectives SARS-CoV-2, causing COVID-19, has emerged to cause a human pandemic. Detection of SARS-CoV-2 in respiratory samples by using PCR is the standard laboratory diagnostic tool. Our aim was to perform a limited evaluation of the diagnostic performance and user-friendliness of eleven rapid tests for detection of antibodies against SARS-CoV-2. Methods All participants were tested with PCR against SARS-CoV-2 at a clinical microbiology laboratory. Comparing with results from PCR tests, we evaluated the rapid tests' performances in three arms; 1) 20 hospitalized patients with PCR-confirmed COVID-19, 2) 23 recovered outpatients with former PCR-confirmed COVID-19, and 3) 49 participants with suspected COVID-19 presenting at a primary care emergency room. Results All eleven tests detected antibodies in hospitalized COVID-19 patients, though with varying sensitivities. In former outpatients recovered from COVID-19, there were differences between tests in the immunoglobulin type G (IgG) sensitivity, with five tests having a sensitivity below 65%. In participants with suspected COVID-19 infection, the rapid tests had very low sensitivities. Most rapid tests were easy to perform and interpret. Conclusions Rapid tests were not suited as stand-alone tests to detect present infection in a Norwegian primary care emergency room population. All the rapid tests were able to detect SARS-CoV-2 antibodies, although sensitivities varied and were generally higher in the study arm of more severely affected participants. Rapid tests with high IgG sensitivity (and specificity) may be useful for confirmation of past infection. An independent evaluation should be performed in the intended population before introducing a rapid test.
Collapse
Affiliation(s)
- Mette C Tollånes
- Norwegian Organization for Quality Improvement of Laboratory Examinations, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Anne-Marte Bakken Kran
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Microbiology, Oslo University Hospital Ullevål, Oslo, Norway
| | | | - Pål A Jenum
- Norwegian Organization for Quality Improvement of Laboratory Examinations, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Anne C Breivik
- Norwegian Organization for Quality Improvement of Laboratory Examinations, Haraldsplass Deaconess Hospital, Bergen, Norway
| | - Sverre Sandberg
- Norwegian Organization for Quality Improvement of Laboratory Examinations, Haraldsplass Deaconess Hospital, Bergen, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Medical Biochemistry and Pharmacology, Haukeland University Hospital, Bergen, Norway
| |
Collapse
|
45
|
Riccò M, Ferraro P, Gualerzi G, Ranzieri S, Bragazzi NL, Balzarini F, Signorelli C. Point-of-Care diagnostic of SARS-CoV-2: knowledge, attitudes, and perceptions (KAP) of medical workforce in Italy. Acta Biomed 2020; 91:57-67. [PMID: 32420926 PMCID: PMC7569620 DOI: 10.23750/abm.v91i2.9573] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 04/22/2020] [Indexed: 12/12/2022]
Abstract
INTRODUCTION The present study aims to characterize knowledge, attitudes and beliefs in a sample of medical professionals towards point-of-care (POC) rapid tests for SARS-CoV-2 in Italy (April 2020). MATERIAL AND METHODS A total of 561 professionals (42.6% males, 26.9% ≥ 50-year-old) compiled a specifically designed web questionnaire on characteristics of POC rapid tests. They were asked whether they would change daily practice and make clinical decisions according to POC tests. Multivariate odds ratios (aOR) for predictors of propensity towards the aforementioned behavioral outcomes were calculated through regression analysis. RESULTS Overall, only 51.9% knew the official recommendations of the Italian Health Authorities for POC tests, while 26.0% of respondents considered POC tests for COVID-19 highly reliable. Still, 40.3% of respondents would change daily practice because of such tests, and 38.5% would make clinical decisions based of their results. Actual understanding of specificity and sensitivity of POC tests was not associated with assessed behavioral outcomes: main positive effectors were identified in perceived reliability and usefulness of rapid tests, acknowledging the existence of official recommendations, understanding the limited clinical implications of POC tests, and working as occupational physicians were characterized as negative effectors. Conclusions. Propensity of sampled professionals towards POC tests for COVID-19 was diffusely unsatisfying. While actual understanding of accuracy of such tests was not a main effector of propensity, previous experiences with other POC tests in daily practice, particularly among occupational physicians may have impaired overall acceptance of such instruments.
Collapse
Affiliation(s)
- Matteo Riccò
- Azienda USL-IRCCS di Reggio Emilia V.le Amendola n.2 - 42122 REServizio di Prevenzione e Sicurezza negli Ambienti di Lavoro (SPSAL)Dip. di Prevenzione.
| | - Pietro Ferraro
- ASL Foggia, Dipartimento di Prevenzione, Servizio Prevenzione e Sicurezza Ambienti Lavoro, Piazza Pavoncelli 11 Foggia (FG), Italy.
| | - Giovanni Gualerzi
- University of Parma, Department of Medicine and Surgery, School of Medicine; Via Gramsci n.14, 43123; Parma (PR), Italy.
| | - Silvia Ranzieri
- University of Parma, Department of Medicine and Surgery, School of Occupational Medicine; Via Gramsci n.14, 43123; Parma (PR), Italy.
| | - Nicola Luigi Bragazzi
- Laboratory for Industrial and Applied Mathematics (LIAM), Department of Mathematics and Statistics, York University, Toronto, Canada.
| | - Federica Balzarini
- University "Vita e Salute", San Raffaele Hospital; Via Olgettina n. 58, 20132; Milan (MI), Italy .
| | - Carlo Signorelli
- University "Vita e Salute", San Raffaele Hospital; Via Olgettina n. 58, 20132; Milan (MI), Italy .
| |
Collapse
|
46
|
Vásárhelyi B, Kristóf K, Ostorházi E, Szabó D, Prohászka Z, Merkely B. The diagnostic value of rapid anti IgM and IgG detecting tests in the identification of patients with SARS CoV-2 virus infection. Orv Hetil 2020; 161:807-812. [PMID: 32364358 DOI: 10.1556/650.2020.31859] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Introduction: At the end of March, 2020, rapid tests detecting the presence of antiviral IgM and IgG antibodies against SARS-CoV-2 virus were introduced in Hungary for the identification of SARS-CoV-2 infection (COVID-19 disease). Aim: We evaluated two rapid tests (Anhui and Clungene) in comparison with those of real-time PCR tests considered as the gold standard in the detection of infection. Method: Between 16, March and 14, April, 2020, we performed rapid IgM and IgG detecting tests without PCR; PCR without rapid tests; and PCR WITH rapid tests in 4140, 3210 and 1654 patients, respectively. (Out of these 1654 patients, Anhui and Clungene tests were used for testing in 625 and 1029 patients, respectively.) Patients were considered as positive in PCR and rapid tests when PCR positivity and IgM or IgG positivity occurred at any time, respectively. (Note: Clungene test is also marketed as 'Lungene'.) Results: The prevalence of PCR positivity in 4864 patients tested with PCR was 6.3%. The sensitivity and specificity of Anhui and Clungene tests were 33.3% and 72.85%, and 35.48% and 85.02%, respectively. At 6% PCR positivity, the positive and negative predictive values of Anhui and Clungene were 7.28%, 94.48%, 13.13%, and 95.38%, respectively. Conclusion: The low positive predictive values indicate that Anhui and Clungene rapid tests detecting the presence of anti-IgM and anti-IgG against SARS-CoV-2 virus infection are not suitable for screening SARS-CoV-2 vírus infection in the general population. These results strongly support that Anhui and Clungene rapid tests detecting IgM and IgG antibodies against SARS-CoV-2 virus should not be used in the differential diagnosis of infection. Orv Hetil. 2020; 161(20): 807-812.
Collapse
|
47
|
Bartosh AV, Sotnikov DV, Hendrickson OD, Zherdev AV, Dzantiev BB. Design of Multiplex Lateral Flow Tests: A Case Study for Simultaneous Detection of Three Antibiotics. Biosensors (Basel) 2020; 10:bios10030017. [PMID: 32120923 PMCID: PMC7146299 DOI: 10.3390/bios10030017] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/11/2020] [Accepted: 02/21/2020] [Indexed: 12/24/2022]
Abstract
The presented study is focused on the impact of binding zone location on immunochromatographic test strips on the analytical parameters of multiplex lateral flow assays. Due to non-equilibrium conditions for such assays the duration of immune reactions influences significantly the analytical parameters, and the integration of several analytes into one multiplex strip may cause an essential decrease of sensitivity. To choose the best location for binding zones, we have tested reactants for immunochromatographic assays of lincomycin, chloramphenicol, and tetracycline. The influence of the distance to the binding zones on the intensity of coloration and limit of detection (LOD) was rather different. Basing on the data obtained, the best order of binding zones was chosen. In comparison with non-optimal location the LODs were 5–10 fold improved. The final assay provides LODs 0.4, 0.4 and 1.0 ng/mL for lincomycin, chloramphenicol, and tetracycline, respectively. The proposed approach can be applied for multiplexed assays of other analytes.
Collapse
|
48
|
Zasada AA. Detection and Identification of Bacillus anthracis: From Conventional to Molecular Microbiology Methods. Microorganisms 2020; 8:E125. [PMID: 31963339 PMCID: PMC7023132 DOI: 10.3390/microorganisms8010125] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 12/31/2019] [Revised: 01/13/2020] [Accepted: 01/15/2020] [Indexed: 02/06/2023] Open
Abstract
Rapid and reliable identification of Bacillus anthracis is of great importance, especially in the event of suspected deliberate release of anthrax spores. However, the identification of B. anthracis is challenging due to its high similarity to closely related species. Since Amerithrax in 2001, a lot of effort has been made to develop rapid methods for detection and identification of this microorganism with special focus on easy-to-perform rapid tests for first-line responders. This article presents an overview of the evolution of B. anthracis identification methods from the time of the first description of the microorganism until the present day.
Collapse
Affiliation(s)
- Aleksandra A Zasada
- Department of Sera and Vaccines Evaluation, National Institute of Public Health-National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland
| |
Collapse
|
49
|
Urusov AE, Zherdev AV, Dzantiev BB. Towards Lateral Flow Quantitative Assays: Detection Approaches. Biosensors (Basel) 2019; 9:E89. [PMID: 31319629 PMCID: PMC6784366 DOI: 10.3390/bios9030089] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [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] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 02/07/2023]
Abstract
Point-of-care (POC) or bedside analysis is a global trend in modern diagnostics. Progress in POC testing has largely been provided by advanced manufacturing technology for lateral flow (immunochromatographic) test strips. They are widely used to rapidly and easily control a variety of biomarkers of infectious diseases and metabolic and functional disorders, as well as in consumer protection and environmental monitoring. However, traditional lateral flow tests rely on visual assessment and qualitative conclusion, which limit the objectivity and information output of the assays. Therefore, there is a need for approaches that retain the advantages of lateral flow assays and provide reliable quantitative information about the content of a target compound in a sample mixture. This review describes the main options for detecting, processing, and interpreting immunochromatographic analysis results. The possibilities of modern portable detectors that register colored, fluorescent, magnetic, and conductive labels are discussed. Prospects for further development in this direction are also examined.
Collapse
Affiliation(s)
- Alexandr E Urusov
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Anatoly V Zherdev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Boris B Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia.
| |
Collapse
|
50
|
Ny P, Ozaki A, Pallares J, Nieberg P, Wong-Beringer A. Antimicrobial Stewardship Opportunities in Patients with Bacteremia Not Identified by BioFire FilmArray. J Clin Microbiol 2019; 57:e01941-18. [PMID: 30814265 DOI: 10.1128/JCM.01941-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/17/2019] [Indexed: 01/02/2023] Open
Abstract
A subset of bacteremia cases are caused by organisms not detected by a rapid-diagnostics platform, BioFire blood culture identification (BCID), with unknown clinical characteristics and outcomes. Patients with ≥1 positive blood culture over a 15-month period were grouped by negative (NB-PC) versus positive (PB-PC) BioFire BCID results and compared with respect to demographics, infection characteristics, antibiotic therapy, and outcomes (length of hospital stay [LOS] and in-hospital mortality). Six percent of 1,044 positive blood cultures were NB-PC. The overall mean age was 65 ± 22 years, 54% of the patients were male, and most were admitted from home; fewer NB-PC had diabetes (19% versus 31%, P = 0.0469), although the intensive care unit admission data were similar. Anaerobes were identified in 57% of the bacteremia cases from the NB-PC group by conventional methods: Bacteroides spp. (30%), Clostridium (11%), and Fusobacterium spp. (8%). Final identification of the NB-PC pathogen was delayed by 2 days (P < 0.01) versus the PB-PC group. The sources of bacteremia were more frequently unknown for the NB-PC group (32% versus 11%, P < 0.01) and of pelvic origin (5% versus 0.1%, P < 0.01) compared to urine (31% versus 9%, P < 0.01) for the PB-PC patients. Fewer NB-PC patients received effective treatment before (68% versus 84%, P = 0.017) and after BCID results (82% versus 96%, P = 0.0048). The median LOS was similar (7 days), but more NB-PC patients died from infection (26% versus 8%, P < 0.01). Our findings affirm the need for the inclusion of anaerobes in BioFire BCID or other rapid diagnostic platforms to facilitate the prompt initiation of effective therapy for bacteremia.
Collapse
|