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Sanchez JL, Cooper MJ, Myers CA, Cummings JF, Vest KG, Russell KL, Sanchez JL, Hiser MJ, Gaydos CA. Respiratory Infections in the U.S. Military: Recent Experience and Control. Clin Microbiol Rev 2015; 28:743-800. [PMID: 26085551 PMCID: PMC4475643 DOI: 10.1128/cmr.00039-14] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
This comprehensive review outlines the impact of military-relevant respiratory infections, with special attention to recruit training environments, influenza pandemics in 1918 to 1919 and 2009 to 2010, and peacetime operations and conflicts in the past 25 years. Outbreaks and epidemiologic investigations of viral and bacterial infections among high-risk groups are presented, including (i) experience by recruits at training centers, (ii) impact on advanced trainees in special settings, (iii) morbidity sustained by shipboard personnel at sea, and (iv) experience of deployed personnel. Utilizing a pathogen-by-pathogen approach, we examine (i) epidemiology, (ii) impact in terms of morbidity and operational readiness, (iii) clinical presentation and outbreak potential, (iv) diagnostic modalities, (v) treatment approaches, and (vi) vaccine and other control measures. We also outline military-specific initiatives in (i) surveillance, (ii) vaccine development and policy, (iii) novel influenza and coronavirus diagnostic test development and surveillance methods, (iv) influenza virus transmission and severity prediction modeling efforts, and (v) evaluation and implementation of nonvaccine, nonpharmacologic interventions.
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Affiliation(s)
- Jose L Sanchez
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | - Michael J Cooper
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | | | - James F Cummings
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | - Kelly G Vest
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | - Kevin L Russell
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA
| | - Joyce L Sanchez
- Mayo Clinic, Division of General Internal Medicine, Rochester, Minnesota, USA
| | - Michelle J Hiser
- Armed Forces Health Surveillance Center, Silver Spring, Maryland, USA Oak Ridge Institute for Science and Education, Postgraduate Research Participation Program, U.S. Army Public Health Command, Aberdeen Proving Ground, Aberdeen, Maryland, USA
| | - Charlotte A Gaydos
- International STD, Respiratory, and Biothreat Research Laboratory, Division of Infectious Diseases, Johns Hopkins University, Baltimore, Maryland, USA
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Neemann K, Freifeld A. Respiratory Syncytial Virus in Hematopoietic Stem Cell Transplantation and Solid-Organ Transplantation. Curr Infect Dis Rep 2015; 17:490. [DOI: 10.1007/s11908-015-0490-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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203
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Emerging technologies for the clinical microbiology laboratory. Clin Microbiol Rev 2015; 27:783-822. [PMID: 25278575 DOI: 10.1128/cmr.00003-14] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In this review we examine the literature related to emerging technologies that will help to reshape the clinical microbiology laboratory. These topics include nucleic acid amplification tests such as isothermal and point-of-care molecular diagnostics, multiplexed panels for syndromic diagnosis, digital PCR, next-generation sequencing, and automation of molecular tests. We also review matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) and electrospray ionization (ESI) mass spectrometry methods and their role in identification of microorganisms. Lastly, we review the shift to liquid-based microbiology and the integration of partial and full laboratory automation that are beginning to impact the clinical microbiology laboratory.
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204
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Economic analysis of rapid and sensitive polymerase chain reaction testing in the emergency department for influenza infections in children. Pediatr Infect Dis J 2015; 34:577-82. [PMID: 25973935 DOI: 10.1097/inf.0000000000000703] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BACKGROUND Rapid multiplex polymerase chain reaction (PCR) assays simultaneously detect several respiratory viral pathogens with high sensitivity. Maximizing detection of influenza at the point of care has the potential to reduce unnecessary antibiotic use, laboratory tests and hospitalizations. However, the cost-effectiveness of rapid multiplex PCR assays for influenza has not been compared with other diagnostic methods in children. METHODS For children presenting to the emergency department with influenza-like illness, we compared costs and outcomes using 4 different testing strategies for detection of influenza: (1) a rapid multiplex PCR platform (FilmArray); (2) traditional PCR; (3) direct-fluorescent antibody and (4) rapid antigen tests. Costs were assessed from the hospital perspective, and effectiveness was defined as quality-adjusted life years (QALYs). Input parameters were obtained from previous studies, and the model was run separately for children aged 3-36 months and 3-18 years. RESULTS Rapid multiplex PCR testing was the most effective testing strategy for children in both age groups. The incremental cost-effectiveness when compared with rapid antigen tests was $115,556 per QALY for children aged 3-36 months and from $228,000 per QALY for children aged 3-18 years. The cost-effectiveness of rapid multiplex PCR was sensitive to estimates for influenza prevalence, the proportion of patients treated with antivirals and the cost per test. CONCLUSIONS Our model identifies scenarios in which identification of influenza in the emergency department using rapid multiplex PCR testing is a cost-effective strategy for infants and children 3 months through 18 years. Including detection of other respiratory viruses in the analysis would further improve cost-effectiveness.
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Enterovirus D68. A Focused Review and Clinical Highlights from the 2014 U.S. Outbreak. Ann Am Thorac Soc 2015; 12:775-81. [DOI: 10.1513/annalsats.201412-592fr] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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206
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Messacar K, Schreiner TL, Maloney JA, Wallace A, Ludke J, Oberste MS, Nix WA, Robinson CC, Glodé MP, Abzug MJ, Dominguez SR. A cluster of acute flaccid paralysis and cranial nerve dysfunction temporally associated with an outbreak of enterovirus D68 in children in Colorado, USA. Lancet 2015; 385:1662-71. [PMID: 25638662 DOI: 10.1016/s0140-6736(14)62457-0] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Clusters of acute flaccid paralysis or cranial nerve dysfunction in children are uncommon. We aimed to assess a cluster of children with acute flaccid paralysis and cranial nerve dysfunction geographically and temporally associated with an outbreak of enterovirus-D68 respiratory disease. METHODS We defined a case of neurological disease as any child admitted to Children's Hospital Colorado (Aurora, CO, USA) with acute flaccid paralysis with spinal-cord lesions involving mainly grey matter on imaging, or acute cranial nerve dysfunction with brainstem lesions on imaging, who had onset of neurological symptoms between Aug 1, 2014, and Oct 31, 2014. We used Poisson regression to assess whether the numbers of cases during the outbreak period were significantly greater than baseline case numbers from a historical control period (July 31, 2010, to July 31, 2014). FINDINGS 12 children met the case definition (median age 11·5 years [IQR 6·75-15]). All had a prodromal febrile illness preceding neurological symptoms by a median of 7 days (IQR 5·75-8). Neurological deficits included flaccid limb weakness (n=10; asymmetric n=7), bulbar weakness (n=6), and cranial nerve VI (n=3) and VII (n=2) dysfunction. Ten (83%) children had confluent, longitudinally extensive spinal-cord lesions of the central grey matter, with predominant anterior horn-cell involvement, and nine (75%) children had brainstem lesions. Ten (91%) of 11 children had cerebrospinal fluid pleocytosis. Nasopharyngeal specimens from eight (73%) of 11 children were positive for rhinovirus or enterovirus. Viruses from five (45%) of 11 children were typed as enterovirus D68. Enterovirus PCR of cerebrospinal fluid, blood, and rectal swabs, and tests for other causes, were negative. Improvement of cranial nerve dysfunction has been noted in three (30%) of ten children. All ten children with limb weakness have residual deficits. INTERPRETATION We report the first geographically and temporally defined cluster of acute flaccid paralysis and cranial nerve dysfunction in children associated with an outbreak of enterovirus-D68 respiratory illness. Our findings suggest the possibility of an association between enterovirus D68 and neurological disease in children. If enterovirus-D68 infections continue to happen in an endemic or epidemic pattern, development of effective antiviral or immunomodulatory therapies and vaccines should become scientific priorities. FUNDING National Center for Advancing Translational Sciences, National Institutes of Health.
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Affiliation(s)
- Kevin Messacar
- Departments of Pediatric Infectious Diseases, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA; Hospital Medicine, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Teri L Schreiner
- Child Neurology, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - John A Maloney
- Radiology, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Adam Wallace
- Child Neurology, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Jan Ludke
- Child Neurology, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - M Stephen Oberste
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - W Allan Nix
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Christine C Robinson
- Pathology and Laboratory Medicine, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Mary P Glodé
- Departments of Pediatric Infectious Diseases, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Mark J Abzug
- Departments of Pediatric Infectious Diseases, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Samuel R Dominguez
- Departments of Pediatric Infectious Diseases, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA.
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Mwaigwisya S, Assiri RAM, O'Grady J. Emerging commercial molecular tests for the diagnosis of bloodstream infection. Expert Rev Mol Diagn 2015; 15:681-92. [PMID: 25866124 DOI: 10.1586/14737159.2015.1029459] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bloodstream infection (BSI) by microorganisms can lead to sepsis. This condition has a high mortality rate, which rises significantly with delays in initiation of appropriate antimicrobial treatment. Current culture methods for diagnosing BSI have long turnaround times and poor clinical sensitivity. While clinicians wait for culture diagnosis, patients are treated empirically, which can result in inappropriate treatment, undesirable side effects and contribute to drug resistance development. Molecular diagnostics assays that target pathogen DNA can identify pathogens and resistance markers within hours. Early diagnosis improves antibiotic stewardship and is associated with favorable clinical outcomes. Nonetheless, limitations of current molecular diagnostic methods are substantial. This article reviews recent commercially available molecular methods that use pathogen DNA to diagnose BSI, either by testing positive blood cultures or directly testing patient blood. We critically assess these tests and their application in clinical microbiology. A view of future directions in BSI diagnosis is also provided.
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Abstract
Molecular diagnostics comprises a main analytical division in clinical laboratory diagnostics. The analysis of RNA or DNA helps to diagnose infectious diseases and identify genetic determined disorders or even cancer. Starting from mono-parametric tests within the last years, technologies have evolved that allow for the detection of many parameters in parallel, e.g., by using multiplex nucleic acid amplification techniques, microarrays, or next-generation sequencing technologies. The introduction of closed-tube systems as well as lab-on-a-chip devices further resulted in a higher automation degree with a reduced contamination risk. These applications complement or even stepwise replace classical methods in clinical microbiology like virus cultures, resistance determination, microscopic and metabolic analyses, as well as biochemical or immunohistochemical assays. In addition, novel diagnostic markers appear, like noncoding RNAs and miRNAs providing additional room for novel biomarkers. This article provides an overview of microarrays as diagnostics devices and research tools. Introduced in 1995 for transcription analysis, microarrays are used today to detect several different biomolecules like DNA, RNA, miRNA, and proteins among others. Mainly used in research, some microarrays also found their way to clinical diagnostics. Further, closed lab-on-a-chip devices that use DNA microarrays as detection tools are discussed, and additionally, an outlook toward applications of next-generation sequencing tools in diagnostics will be given.
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Affiliation(s)
- Volker A. Erdmann
- Free University of Berlin Institute of Chemistry/Biochemistry, Thielallee 63, Berlin Germany
| | - Stefan Jurga
- Nanobiomedical Center, Adam Mickiewicz University, Umultowska 85 Poznań, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Z. Noskowskiego 12/14 Poznań, Poland
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209
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Jerris RC, Williams SR, MacDonald HJ, Ingebrigtsen DR, Westblade LF, Rogers BB. Testing implications of varying targets for Bordetella pertussis: comparison of the FilmArray Respiratory Panel and the Focus B. pertussis PCR assay. J Clin Pathol 2015; 68:394-6. [PMID: 25742911 PMCID: PMC4413735 DOI: 10.1136/jclinpath-2014-202833] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/19/2015] [Indexed: 01/12/2023]
Abstract
BACKGROUND The FilmArray Respiratory Panel (RP) detects multiple pathogens, including Bordetella pertussis. The multiplex PCR system is appropriate for a core laboratory or point of care due to ease of use. The purpose of this study is to compare the analytical sensitivity of the FilmArray RP, which targets the promoter region of the B. pertussis toxin gene, with the Focus real-time PCR assay, which targets the insertion sequence IS481. METHODS Seventy-one specimens from patients aged 1 month to 18 years, which had tested positive for B. pertussis using the Focus assay, were analysed using the FilmArray RP. RESULTS Forty-six specimens were positive for B. pertussis by both the Focus and the FilmArray RP assays. Twenty-five specimens were negative for B. pertussis using the FilmArray RP assay, but positive using the Focus assay. CONCLUSIONS The FilmArray RP assays will detect approximately 1/3 less cases of B. pertussis than the Focus assay.
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Affiliation(s)
- Robert C Jerris
- Children's Healthcare of Atlanta, Atlanta, Georgia, USA Emory University School of Medicine, Atlanta, Georgia, USA
| | | | | | | | - Lars F Westblade
- Children's Healthcare of Atlanta, Atlanta, Georgia, USA Emory University School of Medicine, Atlanta, Georgia, USA
| | - Beverly B Rogers
- Children's Healthcare of Atlanta, Atlanta, Georgia, USA Emory University School of Medicine, Atlanta, Georgia, USA
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210
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Marcone DN, Carballal G, Ricarte C, Echavarria M. [Respiratory viral diagnosis by using an automated system of multiplex PCR (FilmArray) compared to conventional methods]. Rev Argent Microbiol 2015; 47:29-35. [PMID: 25735216 PMCID: PMC7131815 DOI: 10.1016/j.ram.2014.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/23/2014] [Accepted: 12/29/2014] [Indexed: 02/04/2023] Open
Abstract
Las infecciones respiratorias agudas producen una importante morbimortalidad y comúnmente son causadas por virus. En Argentina, los programas de vigilancia epidemiológica se basan en la detección de antígenos virales por inmunofluorescencia (IF), aunque es bien conocido que los métodos moleculares son más sensibles. El panel respiratorio (PR) FilmArray (PR-FilmArray) es un equipo comercial automatizado de PCR múltiples que detecta 17 virus respiratorios y 3 bacterias, en un sistema cerrado que requiere 5 min de procesamiento y una 1 h de instrumentación. Se evaluó un total de 315 muestras respiratorias de niños menores de 6 años con infecciones respiratorias agudas por IF para 8 virus respiratorios y por RT-PCR para rinovirus. Posteriormente, estas muestras se estudiaron con el PR-FilmArray. La frecuencia de positividad al considerar los 9 virus estudiados por IF y RT-PCR fue del 75 %; por PR-FilmArray fue del 92 %. El porcentaje de acuerdo positivo entre ambas metodologías fue del 70,5 % y el de acuerdo negativo fue del 99,6 % (intervalo de confianza 95 %: 65,5-75,1 y 99,2-99,8, respectivamente). El PR-FilmArray permitió obtener un mayor diagnóstico positivo (97 %) y detectó otros virus, como los coronavirus NL63, 229E, OC43 y HKU1 (10 %) y los bocavirus (18 %). Además, permitió identificar coinfecciones múltiples (39 %) con 2, 3, 4 y hasta 5 virus. Actualmente, la IF continúa siendo el método más utilizado en los países latinoamericanos para el diagnóstico de virus respiratorios por su bajo costo, por su capacidad para procesar un alto número de muestras simultáneamente y porque los resultados de los virus más frecuentes están disponibles en 5 h. Sin embargo, la futura incorporación de métodos moleculares aumentaría notablemente la capacidad diagnóstica.
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Affiliation(s)
- Débora N Marcone
- Unidad de Virología (UNVIR-CONICET) y Laboratorio de Virología Clínica, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno (CEMIC), Hospital Universitario, Ciudad Autónoma de Buenos Aires (CABA), Argentina
| | - Guadalupe Carballal
- Unidad de Virología (UNVIR-CONICET) y Laboratorio de Virología Clínica, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno (CEMIC), Hospital Universitario, Ciudad Autónoma de Buenos Aires (CABA), Argentina
| | - Carmen Ricarte
- Unidad de Virología (UNVIR-CONICET) y Laboratorio de Virología Clínica, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno (CEMIC), Hospital Universitario, Ciudad Autónoma de Buenos Aires (CABA), Argentina
| | - Marcela Echavarria
- Unidad de Virología (UNVIR-CONICET) y Laboratorio de Virología Clínica, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno (CEMIC), Hospital Universitario, Ciudad Autónoma de Buenos Aires (CABA), Argentina.
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Das D, Le Floch H, Houhou N, Epelboin L, Hausfater P, Khalil A, Ray P, Duval X, Claessens YE, Leport C. Viruses detected by systematic multiplex polymerase chain reaction in adults with suspected community-acquired pneumonia attending emergency departments in France. Clin Microbiol Infect 2015; 21:608.e1-8. [PMID: 25704448 PMCID: PMC7128919 DOI: 10.1016/j.cmi.2015.02.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 01/25/2015] [Accepted: 02/10/2015] [Indexed: 01/10/2023]
Abstract
UNLABELLED Infectious agents associated with community-acquired pneumonia (CAP) are under-studied. This study attempted to identify viruses from the upper respiratory tract in adults visiting emergency departments for clinically suspected CAP. Adults with suspected CAP enrolled in the ESCAPED study (impact of computed tomography on CAP diagnosis) had prospective nasopharyngeal (NP) samples studied by multiplex PCR (targeting 15 viruses and four intracellular bacteria). An adjudication committee composed of infectious disease specialists, pneumologists and radiologists blinded to PCR results reviewed patient records, including computed tomography and day 28 follow up, to categorize final diagnostic probability of CAP as definite, probable, possible, or excluded. Among the 254 patients enrolled, 78 (31%) had positive PCR, which detected viruses in 72/254 (28%) and intracellular bacteria in 8 (3%) patients. PCR was positive in 44/125 (35%) patients with definite CAP and 21/83 (25%) patients with excluded CAP. The most frequent organisms were influenza A/B virus in 27 (11%), rhinovirus in 20 (8%), coronavirus in seven (3%), respiratory syncytial virus in seven (3%) and Mycoplasma pneumoniae in eight (3%) of 254 patients. Proportion of rhinovirus was higher in patients with excluded CAP compared with other diagnostic categories (p = 0.01). No such difference was observed for influenza virus. Viruses seem common in adults attending emergency departments with suspected CAP. A concomitant clinical, radiological and biological analysis of the patient's chart can contribute to either confirm their role, or suggest upper respiratory tract infection or shedding. Their imputability and impact in early management of CAP deserve further studies. CLINICAL TRIALS REGISTRATION NCT01574066.
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Affiliation(s)
- D Das
- IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; UMR 1137, Inserm, Paris, France
| | - H Le Floch
- Service des Maladies Respiratoires, Hôpital d'Instruction des Armées Percy, Clamart, France
| | - N Houhou
- Service de Virologie, Hôpital Bichat - Claude Bernard, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - L Epelboin
- Service de Maladies Infectieuses et Tropicales, CHU Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris, France; Université Pierre et Marie Curie, Paris, France
| | - P Hausfater
- Université Pierre et Marie Curie, Paris, France; Centre Pitié, Urgences, CHU Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - A Khalil
- Service de Radiologie, Hôpital Tenon, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - P Ray
- Centre Tenon, Urgences, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - X Duval
- IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; UMR 1137, Inserm, Paris, France; CIC 1425, Inserm, Hôpital Bichat - Claude Bernard, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Y-E Claessens
- Département de Médecine d'Urgence, Centre Hospitalier Princesse Grace, Monaco
| | - C Leport
- IAME, UMR 1137, Université Paris Diderot, Sorbonne Paris Cité, Paris, France; UMR 1137, Inserm, Paris, France; Unité de Coordination du Risque Épidémique et Biologique, Assistance Publique - Hôpitaux de Paris, Paris, France.
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212
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Muehlenbachs A, Bhatnagar J, Zaki SR. Tissue tropism, pathology and pathogenesis of enterovirus infection. J Pathol 2015; 235:217-28. [PMID: 25211036 DOI: 10.1002/path.4438] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 09/08/2014] [Accepted: 09/09/2014] [Indexed: 02/04/2023]
Abstract
Enteroviruses are very common and cause infections with a diverse array of clinical features. Enteroviruses are most frequently considered by practising pathologists in cases of aseptic meningitis, encephalitis, myocarditis and disseminated infections in neonates and infants. Congenital infections have been reported and transplacental transmission is thought to occur. Although skin biopsies during hand, foot and mouth disease are infrequently obtained, characteristic dermatopathological findings can be seen. Enteroviruses have been implicated in lower respiratory tract infections. This review highlights histopathological features of enterovirus infection and discusses diagnostic modalities for formalin-fixed paraffin-embedded tissues and their associated pitfalls. Immunohistochemistry can detect enterovirus antigen within cells of affected tissues; however, assays can be non-specific and detect other viruses. Molecular methods are increasingly relied upon but, due to the high frequency of asymptomatic enteroviral infections, clinical-pathological correlation is needed to determine significance. Of note, diagnostic assays on central nervous system or cardiac tissues from immunocompetent patients with prolonged disease courses are most often negative. Histopathological, immunohistochemical and molecular studies performed on clinical specimens also provide insight into enteroviral tissue tropism and pathogenesis.
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Affiliation(s)
- Atis Muehlenbachs
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Chun K, Syndergaard C, Damas C, Trubey R, Mukindaraj A, Qian S, Jin X, Breslow S, Niemz A. Sepsis Pathogen Identification. ACTA ACUST UNITED AC 2015; 20:539-61. [PMID: 25631157 DOI: 10.1177/2211068214567345] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Indexed: 12/29/2022]
Abstract
Sepsis is a rapidly progressing, severe inflammatory response to infection, causing more than 200,000 deaths per year. Rapid, specific pathogen identification is important to guide sepsis treatment. In this review, we describe and compare currently available commercial products for sepsis diagnosis and pathogen identification, based on microbiological, molecular, and mass spectrometric technologies. Microbiological techniques, the current "gold standard" in sepsis pathogen identification, include blood culture followed by subculturing and pathogen identification via biochemical or microscopic means. These methods have been automated but nevertheless require several days to generate results. Alternative technologies, including highly multiplexed PCR-based methods and mass spectrometric approaches, can decrease the required turnaround time. Matrix-assisted laser-desorption ionization time-of-flight-based systems have recently become an attractive option to rapidly identify a broad spectrum of sepsis pathogens with good sensitivity and specificity. Effectively integrating rapid sepsis pathogen identification into the hospital workflow can improve patient outcomes and can reduce the length of hospitalization and cost per patient.
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Affiliation(s)
- Katy Chun
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Chas Syndergaard
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Carlos Damas
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Richard Trubey
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | | | - Shenyu Qian
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Xin Jin
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Scott Breslow
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
| | - Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA, USA
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Hammerschlag MR, Kohlhoff SA, Gaydos CA. Chlamydia pneumoniae. MANDELL, DOUGLAS, AND BENNETT'S PRINCIPLES AND PRACTICE OF INFECTIOUS DISEASES 2015. [PMCID: PMC7173483 DOI: 10.1016/b978-1-4557-4801-3.00184-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
BACKGROUND Effective upstream preparation of nucleic acid (NA) is important for molecular techniques that detect unique DNA or RNA sequences. The isolated NA should be extracted efficiently and purified away from inhibitors of a downstream molecular assay. CONTENT Many NA sample preparation techniques and commercial kits are available. Techniques for cell lysis and isolation or purification of NA were discovered in early NA characterization studies, evolved in the 20th century with molecular techniques, and still serve as the foundation for current methods. Advances in solid phase extraction methods with nonhazardous chemicals and automated systems have changed the way NA is prepared. Factors to consider when selecting NA preparation methods for molecular detection include lysis (from sources as diverse as human cells, viruses, bacterial spores, or protozoan oocysts), DNA vs RNA, sample background, appropriate preparation chemicals, and required detection limits. Methods are also selected on the basis of requirements for a particular application, such as sample volume or removal of inhibitors. Sometimes tradeoffs are made. SUMMARY Good automated and manual methods are available to effectively prepare NA for molecular detection in under an hour. Numerous systems are available for various applications, including techniques that are flexible for multiple sample types, are capable of processing large batches, can be performed in <10 min, or that can yield high-purity NA. When methods are selected using the most applicable combination of lysis isolation efficiency and concentration, NA preparation can be very effective, even for molecular detection of multiple targets from the same sample.
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216
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Affiliation(s)
- Daniel M Musher
- From the Medical Care Line (Infectious Disease Section), Michael E. DeBakey Veterans Affairs Medical Center, and the Departments of Medicine and Molecular Virology and Microbiology, Baylor College of Medicine - both in Houston (D.M.M.); and the Division of Infectious Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston (A.R.T.)
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217
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Abstract
BACKGROUND PCR is a key technology in molecular biology and diagnostics that typically amplifies and quantifies specific DNA fragments in about an hour. However, the kinetic limits of PCR are unknown. METHODS We developed prototype instruments to temperature cycle 1- to 5-μL samples in 0.4-2.0 s at annealing/extension temperatures of 62 °C-76 °C and denaturation temperatures of 85 °C-92 °C. Primer and polymerase concentrations were increased 10- to 20-fold above typical concentrations to match the kinetics of primer annealing and polymerase extension to the faster temperature cycling. We assessed analytical specificity and yield on agarose gels and by high-resolution melting analysis. Amplification efficiency and analytical sensitivity were demonstrated by real-time optical monitoring. RESULTS Using single-copy genes from human genomic DNA, we amplified 45- to 102-bp targets in 15-60 s. Agarose gels showed bright single bands at the expected size, and high-resolution melting curves revealed single products without using any "hot start" technique. Amplification efficiencies were 91.7%-95.8% by use of 0.8- to 1.9-s cycles with single-molecule sensitivity. A 60-bp genomic target was amplified in 14.7 s by use of 35 cycles. CONCLUSIONS The time required for PCR is inversely related to the concentration of critical reactants. By increasing primer and polymerase concentrations 10- to 20-fold with temperature cycles of 0.4-2.0 s, efficient (>90%), specific, high-yield PCR from human DNA is possible in <15 s. Extreme PCR demonstrates the feasibility of while-you-wait testing for infectious disease, forensics, and any application where immediate results may be critical.
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Affiliation(s)
- Jared S Farrar
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT; Current affiliation: MD-PhD Program, Virginia Commonwealth University, Richmond, VA
| | - Carl T Wittwer
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT;
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218
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Stockmann C, Rogatcheva M, Harrel B, Vaughn M, Crisp R, Poritz M, Thatcher S, Korgenski EK, Barney T, Daly J, Pavia AT. How well does physician selection of microbiologic tests identify Clostridium difficile and other pathogens in paediatric diarrhoea? Insights using multiplex PCR-based detection. Clin Microbiol Infect 2014; 21:179.e9-15. [PMID: 25599941 DOI: 10.1016/j.cmi.2014.07.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 07/07/2014] [Accepted: 07/14/2014] [Indexed: 12/22/2022]
Abstract
The objective of this study was to compare the aetiologic yield of standard-of-care microbiologic testing ordered by physicians with that of a multiplex PCR platform. Stool specimens obtained from children and young adults with gastrointestinal illness were evaluated by standard laboratory methods and a developmental version of the FilmArray Gastrointestinal (GI) Diagnostic System (FilmArray GI Panel), a rapid multiplex PCR platform that detects 23 bacterial, viral and protozoal agents. Results were classified according to the microbiologic tests requested by the treating physician. A median of three (range 1-10) microbiologic tests were performed by the clinical laboratory during 378 unique diarrhoeal episodes. A potential aetiologic agent was identified in 46% of stool specimens by standard laboratory methods and in 65% of specimens tested using the FilmArray GI Panel (p < 0.001). For those patients who only had Clostridium difficile testing requested, an alternative pathogen was identified in 29% of cases with the FilmArray GI Panel. Notably, 11 (12%) cases of norovirus were identified among children who only had testing for Clostridium difficile ordered. Among those who had C. difficile testing ordered in combination with other tests, an additional pathogen was identified in 57% of stool specimens with the FilmArray GI Panel. For patients who had no C. difficile testing performed, the FilmArray GI Panel identified a pathogen in 63% of cases, including C. difficile in 8%. Physician-specified laboratory testing may miss important diarrhoeal pathogens. Additionally, standard laboratory testing is likely to underestimate co-infections with multiple infectious diarrhoeagenic agents.
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Affiliation(s)
- C Stockmann
- Department of Pediatrics, University of Utah Health Sciences Center, Salt Lake City, UT, USA.
| | - M Rogatcheva
- BioFire Diagnostics Inc., Salt Lake City, UT, USA
| | - B Harrel
- BioFire Diagnostics Inc., Salt Lake City, UT, USA
| | - M Vaughn
- BioFire Diagnostics Inc., Salt Lake City, UT, USA
| | - R Crisp
- BioFire Diagnostics Inc., Salt Lake City, UT, USA
| | - M Poritz
- BioFire Diagnostics Inc., Salt Lake City, UT, USA
| | - S Thatcher
- BioFire Diagnostics Inc., Salt Lake City, UT, USA
| | - E K Korgenski
- Primary Children's Hospital, Intermountain Healthcare, Salt Lake City, UT, USA
| | - T Barney
- Primary Children's Hospital, Intermountain Healthcare, Salt Lake City, UT, USA
| | - J Daly
- Primary Children's Hospital, Intermountain Healthcare, Salt Lake City, UT, USA; Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, USA
| | - A T Pavia
- Department of Pediatrics, University of Utah Health Sciences Center, Salt Lake City, UT, USA
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219
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Andersson ME, Olofsson S, Lindh M. Comparison of the FilmArray assay and in-house real-time PCR for detection of respiratory infection. ACTA ACUST UNITED AC 2014; 46:897-901. [PMID: 25288382 DOI: 10.3109/00365548.2014.951681] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Recently, molecular methods capable of detecting almost all microbial agents that may cause acute respiratory infection have been introduced. The FilmArray Respiratory Panel assay, which integrates nucleic acid extraction, nested amplification and detection in a reaction pouch preloaded with all reagents required for detection of 17 viruses and 3 bacteria, was compared with an in-house real-time PCR that detects these agents in 8 parallel amplifications. When 128 clinical samples representing 18 of these agents were analysed by both assays the agreement was excellent, with kappa values ranging between 0.54 and 1.0. Discordances were mainly observed for adenovirus, but not when version 1.7 of FilmArray was used. The results show that these assays detect a wide range of pathogens with similar performance. FilmArray provides results after approximately 1 h, including ≈ 5 min hands-on time, and does not require advanced equipment or expertise in molecular diagnostics, making it a useful point-of-care-test for acute respiratory infections.
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Affiliation(s)
- Maria E Andersson
- Department of Infectious Diseases, University of Gothenburg , Gothenburg , Sweden
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220
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Microfluidic quantitative PCR for simultaneous quantification of multiple viruses in environmental water samples. Appl Environ Microbiol 2014; 80:7505-11. [PMID: 25261510 DOI: 10.1128/aem.02578-14] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
To secure food and water safety, quantitative information on multiple pathogens is important. In this study, we developed a microfluidic quantitative PCR (MFQPCR) system to simultaneously quantify 11 major human viral pathogens, including adenovirus, Aichi virus, astrovirus, enterovirus, human norovirus, rotavirus, sapovirus, and hepatitis A and E viruses. Murine norovirus and mengovirus were also quantified in our MFQPCR system as a sample processing control and an internal amplification control, respectively. River water contaminated with effluents from a wastewater treatment plant in Sapporo, Japan, was collected and used to validate our MFQPCR system for multiple viruses. High-throughput quantitative information was obtained with a quantification limit of 2 copies/μl of cDNA/DNA. Using this MFQPCR system, we could simultaneously quantify multiple viral pathogens in environmental water samples. The viral quantities obtained using MFQPCR were similar to those determined by conventional quantitative PCR. Thus, the MFQPCR system developed in this study can provide direct and quantitative information for viral pathogens, which is essential for risk assessments.
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221
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Desoubeaux G, Franck-Martel C, Bailly É, Le Brun C, Gyan E, Goudeau A, Chandenier J, Lanotte P. Prospective assessment of FilmArray® technology for the rapid identification of yeast isolated from blood cultures. J Microbiol Methods 2014; 106:119-122. [PMID: 25192843 DOI: 10.1016/j.mimet.2014.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 08/22/2014] [Accepted: 08/22/2014] [Indexed: 12/22/2022]
Abstract
We prospectively assessed the ability of FilmArray® device to identify fungal species involved in bloodstream infections. It succeeded in identifying 85.7% of isolates. The automated readout of results enabled the rapid initiation of appropriate antifungal therapy. Thus, FilmArray® appeared as a reliable alternative diagnostic method for the most common yeast-like species.
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Affiliation(s)
- Guillaume Desoubeaux
- CHU de Tours, Service de Parasitologie, Mycologie, Médecine tropicale, Tours, France; Université François Rabelais, CEPR-INSERM U1100/E.A. 6305, Faculté de Médecine, Tours, France.
| | - Claire Franck-Martel
- CHU de Tours, Service de Parasitologie, Mycologie, Médecine tropicale, Tours, France
| | - Éric Bailly
- CHU de Tours, Service de Parasitologie, Mycologie, Médecine tropicale, Tours, France
| | - Cécile Le Brun
- CHU de Tours, Laboratoire de Bactériologie, Tours, France
| | - Emmanuel Gyan
- CHU de Tours, Service d'Hématologie clinique, Tours, France; Université François Rabelais, N2C-INSERM U1069, Faculté de Médecine, Tours, France
| | - Alain Goudeau
- CHU de Tours, Laboratoire de Bactériologie, Tours, France; Université François Rabelais, E5 "Bactéries et risque materno-fœtal", UMR 1282 ISP, INRA, Nouzilly, France
| | - Jacques Chandenier
- CHU de Tours, Service de Parasitologie, Mycologie, Médecine tropicale, Tours, France; Université François Rabelais, CEPR-INSERM U1100/E.A. 6305, Faculté de Médecine, Tours, France
| | - Philippe Lanotte
- CHU de Tours, Laboratoire de Bactériologie, Tours, France; Université François Rabelais, E5 "Bactéries et risque materno-fœtal", UMR 1282 ISP, INRA, Nouzilly, France
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Zumla A, Al-Tawfiq JA, Enne VI, Kidd M, Drosten C, Breuer J, Muller MA, Hui D, Maeurer M, Bates M, Mwaba P, Al-Hakeem R, Gray G, Gautret P, Al-Rabeeah AA, Memish ZA, Gant V. Rapid point of care diagnostic tests for viral and bacterial respiratory tract infections--needs, advances, and future prospects. THE LANCET. INFECTIOUS DISEASES 2014; 14:1123-1135. [PMID: 25189349 PMCID: PMC7106435 DOI: 10.1016/s1473-3099(14)70827-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Respiratory tract infections rank second as causes of adult and paediatric morbidity and mortality worldwide. Respiratory tract infections are caused by many different bacteria (including mycobacteria) and viruses, and rapid detection of pathogens in individual cases is crucial in achieving the best clinical management, public health surveillance, and control outcomes. Further challenges in improving management outcomes for respiratory tract infections exist: rapid identification of drug resistant pathogens; more widespread surveillance of infections, locally and internationally; and global responses to infections with pandemic potential. Developments in genome amplification have led to the discovery of several new respiratory pathogens, and sensitive PCR methods for the diagnostic work-up of these are available. Advances in technology have allowed for development of single and multiplexed PCR techniques that provide rapid detection of respiratory viruses in clinical specimens. Microarray-based multiplexing and nucleic-acid-based deep-sequencing methods allow simultaneous detection of pathogen nucleic acid and multiple antibiotic resistance, providing further hope in revolutionising rapid point of care respiratory tract infection diagnostics.
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Affiliation(s)
- Alimuddin Zumla
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Center, University College London Hospitals, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK; Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia; UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia.
| | | | - Virve I Enne
- Division of Infection and Immunity, University College London, London, UK
| | - Mike Kidd
- Division of Infection and Immunity, University College London, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Christian Drosten
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - Judy Breuer
- Division of Infection and Immunity, University College London, London, UK; NIHR Biomedical Research Center, University College London Hospitals, London, UK; Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Marcel A Muller
- Institute of Virology, University of Bonn Medical Centre, Bonn, Germany
| | - David Hui
- Division of Respiratory Medicine and Stanley Ho Center for emerging Infectious Diseases, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Hong Kong
| | - Markus Maeurer
- Therapeutic Immunology, Departments of Laboratory Medicine and Microbiology, Tumour and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Matthew Bates
- Division of Infection and Immunity, University College London, London, UK; UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Peter Mwaba
- UNZA-UCLMS Research and Training Project, University Teaching Hospital, Lusaka, Zambia
| | - Rafaat Al-Hakeem
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | - Gregory Gray
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, USA
| | - Philippe Gautret
- Assistance Publique Hôpitaux de Marseille, CHU Nord, Pôle Infectieux, Institut Hospitalo-Universitaire Méditerranée Infection & Aix Marseille Université, Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), Marseille, France
| | - Abdullah A Al-Rabeeah
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia
| | - Ziad A Memish
- Global Center for Mass Gatherings Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia; Al-Faisal University, Riyadh, Saudi Arabia
| | - Vanya Gant
- Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, UK
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223
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Characterization of human coronavirus OC43 and human coronavirus NL63 infections among hospitalized children <5 years of age. Pediatr Infect Dis J 2014; 33:814-20. [PMID: 24577040 DOI: 10.1097/inf.0000000000000292] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Multiplex molecular assays now make it possible for clinical laboratories to detect human coronaviruses (HCoVs). We investigated the clinical characteristics of HCoV-OC43 and HCoV-NL63 in patients <5 years of age during a recent coronavirus season. METHODS Respiratory viruses were detected using a multiplex molecular assay at St. Louis Children`s Hospital starting in November 2012. We analyzed demographic and clinical data from all patients <5 years of age with solo detection of HCoV-OC43 (n = 52) and HCoV-NL63 (n = 44) and for comparison, samples of children with respiratory syncytial virus, parainfluenza virus and picornaviruses. RESULTS During the study period, HCoV-OC43 (4%) was the 5th and HCoV-NL63 the 8th (2%) most common respiratory virus. Coinfections were detected in 35% and 38% of children with HCoV-OC43 and HCoV-NL63, respectively. Croup was more common with HCoV-NL63 (30%) than with HCoV-OC43 (2%). Lower respiratory tract infection occurred in 33% of children with HCoV-OC43 and 25% of children with HCoV-NL63. Severe illness was less common in HCoV-NL63, HCoV-OC43 and parainfluenza virus (14%, each) compared with respiratory syncytial virus (30%) and picornaviruses (26%; P = 0.055 for HCoVs combined compared with the other respiratory viruses) and occurred mainly in those with underlying medical conditions. CONCLUSIONS Infections caused by HCoV-OC43 and HCoV-NL63 are common and include some with lower respiratory tract involvement and severe disease, especially in children with underlying medical conditions. Overall, a substantial burden of disease associated with both HCoV-OC43 and HCoV-NL63 was observed for hospitalized children <5 years of age.
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224
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Babady NE. The FilmArray® respiratory panel: an automated, broadly multiplexed molecular test for the rapid and accurate detection of respiratory pathogens. Expert Rev Mol Diagn 2014; 13:779-88. [PMID: 24151847 PMCID: PMC7103684 DOI: 10.1586/14737159.2013.848794] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The FilmArray Respiratory Panel (RP) (BioFire(™) Diagnostics, Inc., Salt Lake City, UT, USA) is the first multiplex molecular panel cleared by the US FDA for the detection of both bacterial and viral respiratory pathogens in nasopharygeal swabs. The FilmArray RP targets 20 pathogens including 17 viruses and subtypes and three bacteria, and is performed with minimal sample manipulation. The FilmArray RP has a fully automated sample-to-answer workflow with a turn-around-time of approximately 1 h. The reported sensitivity and specificity of the assay ranges from 80 to 100 and 100%, respectively, with the sensitivity for the adenovirus as low as 46%. A new version of the FilmArray RP assay (version 1.7) with improved sensitivity for the adenovirus was released in 2013. The performance characteristics and simplified workflow have allowed its implementation in a wide range of laboratories. The FilmArray RP has changed the diagnostic landscape and will have a significant impact on the care of patients with respiratory tract infection.
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Affiliation(s)
- N Esther Babady
- Department of Laboratory Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, S428D, New York, NY, 10044, USA
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225
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Identification of microorganisms by FilmArray and matrix-assisted laser desorption ionization-time of flight mass spectrometry prior to positivity in the blood culture system. J Clin Microbiol 2014; 52:3230-6. [PMID: 24951811 DOI: 10.1128/jcm.01084-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In this study, we investigated the performance of the FilmArray and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in identifying microorganisms from blood culture (BC) bottles prior to positivity. First, we used simulated BacT/Alert FA Plus BC bottles with five each for Escherichia coli and Staphylococcus aureus isolates. The FilmArray identified all 10 isolates before BC positivity with 9/10 at 5 h and 1 at 7.5 h after incubation in the BC system. MALDI-TOF MS failed to identify the isolates prior to positivity. When the bottles were incubated for 2.5 h at room temperature (RT) before we put them into the BC system, the FilmArray identified 6/10 at 2.5 h and the remaining 4 at 5 h. Finally, we tested simulated BC bottles after incubation at RT. Interestingly, 9/10 isolates were identified with the FilmArray after 8 h of incubation at RT. Second, we studied clinical BC bottles in quadruplicate. When three-fourths of the parallel bottles signaled positive, the FilmArray was run on the fourth nonsignaled bottle and was found to be positive in 14/15 such cases. Third, we analyzed the performance of the FilmArray in the identification of microorganisms from clinical BC bottles before incubation in the system. Two milliliters of broth from 400 BC bottles was collected after arrival at the laboratory and stored at -70°C. Sixteen bottles later signaled positive in the system. When the frozen broth from these bottles was analyzed, the FilmArray identified all the microorganisms in 8/16 bottles prior to incubation in the BC system. This study shows that the FilmArray can identify microorganisms from BC bottles prior to positivity and in some cases even prior to incubation in the BC system.
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226
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Wang J, Simons DB, Adams JL, Jerris RC, Rogers BB. Multiplex viral polymerase chain reaction testing using the FilmArray device compared with direct fluorescent antibody testing. Lab Med 2014; 45:62-4. [PMID: 24719989 DOI: 10.1309/lmomixq6n4japdx1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Advances in fluidics, electronics, and instrument design have enabled automation of complex molecular assays. The FilmArray Respiratory Panel (RP) is one such assay; it allows for rapid detection of multiple viral and bacterial respiratory targets via nested polymerase chain reaction (PCR), with all components contained within a single pouch. We performed a detailed comparison of workflow between the FilmArray RP and direct fluorescent antibody (DFA) staining. The FilmArray RP proved to be more efficient, with as few as 91 total touches needed and as little as 4 minutes 52 seconds hands-on time. This compares with as many as 502 total touches and 12 minutes 45 seconds hands-on time for DFA staining. FilmArray RP detected a greater number of organisms (20 viruses and bacteria vs 7 viruses for DFA staining) and required less training compared with DFA staining. The ease of use of the FilmArray RP makes this molecular assay amenable to operation 24 hours a day, 7 days a week in routine laboratory and point-of-care settings.
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227
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Evaluation of Curetis Unyvero, a multiplex PCR-based testing system, for rapid detection of bacteria and antibiotic resistance and impact of the assay on management of severe nosocomial pneumonia. J Clin Microbiol 2014; 52:2487-92. [PMID: 24789196 DOI: 10.1128/jcm.00325-14] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Health care-associated pneumonia due to multidrug-resistant organisms represents a major therapeutic challenge. Unfortunately, treatment is dependent on empirical therapy, which often leads to improper and inadequate antimicrobial therapy. A rapid multiplex PCR-based Unyvero pneumonia application (UPA) assay that assists in timely decision-making has recently become available. In this study, we evaluated the performance of UPA in detecting etiological pathogens and resistance markers in patients with nosocomial pneumonia (NP). The impact of this assay on the management of severe nosocomial pneumonia was also assessed. Appropriate specimens were processed by UPA according to the manufacturer's protocol in parallel with conventional culture methods. Of the 56 patients recruited into the study, 49 (87.5%) were evaluable. Of these, 27 (55.1%) and 4 (8.2%) harbored multiple bacteria by the PCR assay and conventional culture, respectively. A single pathogen was detected in 8 (16.3%) and 4 (8.2%) patients, respectively. Thirteen different genes were detected from 38 patients, including the ermB gene (40.8%), the blaOXA-51-like gene (28.6%), the sul1 (28.6%) and int1 (20.4%) integrase genes, and the mecA and blaCTX-M genes (12.3% each). The time from sample testing to results was 4 h versus 48 to 96 h by UPA and culture, respectively. Initial empirical treatment was changed within 5 to 6 h in 33 (67.3%) patients based on the availability of UPA results. Thirty (62.2%) of the patients improved clinically. A total of 3 (6.1%) patients died, mainly from their comorbidities. These data demonstrate the potential of a multiplex PCR-based assay for accurate and timely detection of etiological agents of NP, multidrug-resistant (MDR) organisms, and resistance markers, which can guide clinicians in making early antibiotic adjustments.
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228
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Abstract
RT-isoPCR provides multiplex amplification of mRNA targets using a first-stage multiplex RT-PCR reaction with subsequent isothermal amplification for individual target loci detection. We demonstrate detection of 24 mRNA targets with high specificity and sensitivity without compromising sample variation or introducing biases between targets.
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229
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Abstract
Over the past several years a wide variety of molecular assays for the detection of respiratory viruses has reached the market. The tests described herein range from kits containing primers and probes detecting specific groups of viruses, to self-contained systems requiring specialized instruments that extract nucleic acids and perform the polymerase chain reaction with little operator input. Some of the tests target just the viruses involved in large yearly epidemics such as influenza, or specific groups of viruses such as the adenoviruses or parainfluenza viruses; others can detect most of the known respiratory viruses and some bacterial agents.
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230
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Tuite N, Reddington K, Barry T, Zumla A, Enne V. Rapid nucleic acid diagnostics for the detection of antimicrobial resistance in Gram-negative bacteria: is it time for a paradigm shift? J Antimicrob Chemother 2014; 69:1729-33. [PMID: 24677160 DOI: 10.1093/jac/dku083] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A key component for tackling the ever more serious antimicrobial resistance problem in Gram-negative bacteria is the introduction of rapid nucleic acid diagnostics. Successful incorporation of new diagnostic technologies has the potential benefit of improving not only patient treatment but also infection control and antimicrobial stewardship. However, there are still many hurdles to overcome, such as the complexity of resistance mechanisms in Gram-negative bacteria, the discrepancy between phenotype and genotype and the difficulty in distinguishing pathogens from background commensals. A small number of manufacturers have introduced tests to the market that concentrate partly or specifically on resistance determinants in Gram-negative bacteria. These are currently predominantly based on different types of PCR technology. The development of new technologies, such as whole-genome sequencing and the combination of MALDI-TOF with PCR, holds much promise for the introduction of improved diagnostics for the future.
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Affiliation(s)
- Nina Tuite
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Kate Reddington
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Thomas Barry
- Nucleic Acid Diagnostics Research Laboratory (NADRL), Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Alimuddin Zumla
- Department for Clinical Microbiology, 2nd Floor Royal Free Hospital, University College London, Rowland Hill St., London NW3 2PF, UK
| | - Virve Enne
- Department for Clinical Microbiology, 2nd Floor Royal Free Hospital, University College London, Rowland Hill St., London NW3 2PF, UK
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Abstract
The pathogenetic mechanisms leading to asthma are likely to be diverse, influenced by multiple genetic polymorphisms as well as elements of the environment. Recent data on the microbiome of the airway have revealed intriguing differences between the number and diversity of microbial populations in healthy persons and asthmatics. There is convincing evidence that early viral infections, particularly with human rhinovirus and respiratory syncytial virus, are often associated with the development of chronic asthma and with exacerbations. Recent studies suggest that two unrelated types of atypical bacteria, Mycoplasma pneumoniae (Mpn) and Chlamydia pneumoniae, are present in the airways of a substantial proportion of the population, bringing up the possibility that the persistent presence of the organism may contribute to the asthmatic phenotype in a subset of patients. This review will examine the current data regarding a possible role for infection in chronic asthma with a particular focus on atypical bacterial infections.
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Affiliation(s)
- T Prescott Atkinson
- Children's of Alabama CPP M220, 1601 4th Ave South, Birmingham, AL, 35233, USA,
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232
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Poritz MA, Ririe KM. Getting things backwards to prevent primer dimers. J Mol Diagn 2014; 16:159-62. [PMID: 24457120 DOI: 10.1016/j.jmoldx.2014.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 12/30/2013] [Accepted: 01/09/2014] [Indexed: 02/04/2023] Open
Abstract
This Commentary highlights the article by Satterfield that describes a new class of primer technology-cooperative primers, which prevent primer-dimer amplification.
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233
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Lemieux B, Li Y, Kong H, Tang YW. Near instrument-free, simple molecular device for rapid detection of herpes simplex viruses. Expert Rev Mol Diagn 2014; 12:437-43. [DOI: 10.1586/erm.12.34] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Bertrand Lemieux
- BioHelix Corporation, 500 Cummings Center, Suite 5550, Beverly, MA 01915, USA
| | - Ying Li
- BioHelix Corporation, 500 Cummings Center, Suite 5550, Beverly, MA 01915, USA
| | - Huimin Kong
- BioHelix Corporation, 500 Cummings Center, Suite 5550, Beverly, MA 01915, USA
| | - Yi-Wei Tang
- Clinical Microbiology Service, Memorial Sloan–Kettering Cancer Center, 1275 York Avenue, S428, New York, NY 10065, USA
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234
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GRAY J, COUPLAND LJ. The increasing application of multiplex nucleic acid detection tests to the diagnosis of syndromic infections. Epidemiol Infect 2014; 142:1-11. [PMID: 24093495 PMCID: PMC9152551 DOI: 10.1017/s0950268813002367] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 08/30/2013] [Accepted: 08/30/2013] [Indexed: 02/04/2023] Open
Abstract
On 14 January 2013, the US Food and Drug Administration (FDA) announced permission for a multiplex nucleic acid test, the xTAG® Gastrointestinal Pathogen Panel (GPP) (Luminex Corporation, USA), which simultaneously detects 11 common viral, bacterial and parasitic causes of infectious gastroenteritis, to be marketed in the USA. This announcement reflects the current move towards the development and commercialization of detection technologies based on nucleic acid amplification techniques for diagnosis of syndromic infections. We discuss the limitations and advantages of nucleic acid amplification techniques and the recent advances in Conformité Européene - in-vitro diagnostic (CE-IVD)-approved multiplex real-time PCR kits for the simultaneous detection of multiple targets within the clinical diagnostics market.
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Affiliation(s)
- J. GRAY
- Norwich Medical School, University of East Anglia, NRP Innovation Centre, Norwich Research Park, Norwich, Norfolk, UK
- Specialist Virology Centre, Department of Microbiology, Norfolk and Norwich University Hospitals NHS Foundation Trust, NRP Innovation Centre, Norwich Research Park, Norwich, Norfolk, UK
| | - L. J. COUPLAND
- Specialist Virology Centre, Department of Microbiology, Norfolk and Norwich University Hospitals NHS Foundation Trust, NRP Innovation Centre, Norwich Research Park, Norwich, Norfolk, UK
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235
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Jakupciak JP, Wells JM, Karalus RJ, Pawlowski DR, Lin JS, Feldman AB. Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis. J Nucleic Acids 2013; 2013:801505. [PMID: 24455204 PMCID: PMC3877622 DOI: 10.1155/2013/801505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/01/2013] [Accepted: 10/02/2013] [Indexed: 11/18/2022] Open
Abstract
Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations.
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Affiliation(s)
| | | | | | | | - Jeffrey S. Lin
- The Johns Hopkins University, Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
| | - Andrew B. Feldman
- The Johns Hopkins University, Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
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236
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Advances in multiparametric molecular diagnostics technologies for respiratory tract infections. Curr Opin Pulm Med 2013; 19:298-304. [PMID: 23425918 DOI: 10.1097/mcp.0b013e32835f1b32] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW Respiratory tract infections (RTIs) are caused by a variety of bacterial, viral, fungal, and other pathogens and cause millions of deaths each year. Current standard microbiological culture-based tests are laborious and time consuming. Thus, patients are initially treated empirically, leading to inappropriate use of antibiotics. The purpose of this article is to provide clinicians and scientists with a review of recently available commercial multiparametric molecular diagnostics tests for the detection of RTIs so that they can be considered for use instead of, or in combination with, traditional culture techniques. RECENT FINDINGS Several technologies have become commercially available for the multiparametric molecular detection of RTIs in the past decade including tests based on PCR-array, PCR-mass spectrometry, and multiplex qPCR technologies. The majority of these tests are for the detection of viruses, but more recently companies have begun to focus on detection of viruses, bacteria, and associated drug resistances in a single product to maximize the information provided to the clinician by a single test. SUMMARY We describe the recent advances in commercial multiparametric molecular diagnostics technologies for the diagnosis of RTIs. Combining the specific and sensitive molecular detection of bacteria, viruses, fungi, and drug resistances is key if molecular methods are to replace traditional culture. The reliability of the molecular drug-resistance markers chosen, the need for the quantitative detection of some organisms, and throughput are also important considerations for new technology developers.
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237
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Lupo A, Papp-Wallace KM, Sendi P, Bonomo RA, Endimiani A. Non-phenotypic tests to detect and characterize antibiotic resistance mechanisms in Enterobacteriaceae. Diagn Microbiol Infect Dis 2013; 77:179-94. [PMID: 24091103 DOI: 10.1016/j.diagmicrobio.2013.06.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Accepted: 06/12/2013] [Indexed: 02/07/2023]
Abstract
In the past 2 decades, we have observed a rapid increase of infections due to multidrug-resistant Enterobacteriaceae. Regrettably, these isolates possess genes encoding for extended-spectrum β-lactamases (e.g., blaCTX-M, blaTEM, blaSHV) or plasmid-mediated AmpCs (e.g., blaCMY) that confer resistance to last-generation cephalosporins. Furthermore, other resistance traits against quinolones (e.g., mutations in gyrA and parC, qnr elements) and aminoglycosides (e.g., aminoglycosides modifying enzymes and 16S rRNA methylases) are also frequently co-associated. Even more concerning is the rapid increase of Enterobacteriaceae carrying genes conferring resistance to carbapenems (e.g., blaKPC, blaNDM). Therefore, the spread of these pathogens puts in peril our antibiotic options. Unfortunately, standard microbiological procedures require several days to isolate the responsible pathogen and to provide correct antimicrobial susceptibility test results. This delay impacts the rapid implementation of adequate antimicrobial treatment and infection control countermeasures. Thus, there is emerging interest in the early and more sensitive detection of resistance mechanisms. Modern non-phenotypic tests are promising in this respect, and hence, can influence both clinical outcome and healthcare costs. In this review, we present a summary of the most advanced methods (e.g., next-generation DNA sequencing, multiplex PCRs, real-time PCRs, microarrays, MALDI-TOF MS, and PCR/ESI MS) presently available for the rapid detection of antibiotic resistance genes in Enterobacteriaceae. Taking into account speed, manageability, accuracy, versatility, and costs, the possible settings of application (research, clinic, and epidemiology) of these methods and their superiority against standard phenotypic methods are discussed.
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Affiliation(s)
- Agnese Lupo
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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238
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Clinical evaluation of the FilmArray blood culture identification panel in identification of bacteria and yeasts from positive blood culture bottles. J Clin Microbiol 2013; 51:4130-6. [PMID: 24088863 DOI: 10.1128/jcm.01835-13] [Citation(s) in RCA: 194] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The FilmArray platform (FA; BioFire, Salt Lake City, UT) is a closed diagnostic system allowing high-order multiplex PCR analysis with automated readout of results directly from positive blood cultures in 1 h. In the present study, we evaluated the clinical performance of the FilmArray blood culture identification (BCID) panel, which includes 19 bacteria, five yeasts, and three antibiotic resistance genes. In total, 206 blood culture bottles were included in the study. The FilmArray could identify microorganisms in 153/167 (91.6%) samples with monomicrobial growth. Thirteen of the 167 (7.8%) microorganisms were not covered by the FilmArray BCID panel. In 6/167 (3.6%) samples, the FilmArray detected an additional microorganism compared to blood culture. When polymicrobial growth was analyzed, the FilmArray could detect all target microorganisms in 17/24 (71%) samples. Twelve blood culture bottles that yielded a positive signal but showed no growth were also negative by FilmArray. In 3/206 (1.5%) bottles, the FilmArray results were invalid. The results of the FilmArray were reproducible, as demonstrated by the testing and retesting of five bottles in the same day and a longitudinal follow-up of five other blood cultures up to 4 weeks. The present study shows that the FilmArray is a rapid identification method with high performance in direct identification of bacteria and yeasts from positive blood culture bottles.
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239
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McGrath EJ, Thomas R, Asmar B, Fairfax MR, Lephart P, Ameli J, Abdel-Haq N, Salimnia H. Detection of respiratory coinfections in pediatric patients using a small volume polymerase chain reaction array respiratory panel: more evidence for combined droplet and contact isolation. Am J Infect Control 2013; 41:868-73. [PMID: 23510664 PMCID: PMC7115341 DOI: 10.1016/j.ajic.2013.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 12/19/2012] [Accepted: 01/03/2013] [Indexed: 01/04/2023]
Abstract
BACKGROUND In fall 2009, Children's Hospital of Michigan (CHM) instituted combined isolation precautions (contact and droplet isolation) for pediatric inpatients with upper respiratory infection (URI) symptoms to prevent health care-associated infection. METHODS Pediatric patients with symptoms of URI had nasopharyngeal (NP) swab samples obtained prospectively between January and April and September and December 2010 for small volume polymerase chain reaction (SVPCR) array respiratory panel (RP) multiplex nucleic acid testing. NP swabs or nasal washes were obtained for viral culture and rapid antigen testing (RAT). RESULTS Of 499 evaluable SVPCR array RP samples, 344 (69%) tested positive for at least 1 of the 21 tested organisms. The most commonly identified pathogen was rhinovirus/enterovirus (181/344 [53%]) for which no RAT exists at CHM. Of 344 positive specimens, 57 (17%) had at least 2 identified pathogens; 8 (2%) of these had 3. In 11% of patients, molecular testing detected pathogens or pathogen combinations requiring both contact and droplet precautions. CONCLUSION SVPCR array RP testing detected respiratory pathogens in pediatric patients with URI at rates higher than that of RAT and viral culture. Because of the pathogens and pathogen combinations detected, the study findings suggest that combined contact and droplet isolation precautions may be warranted to prevent health care-associated infection in pediatric inpatients with URI. Further studies will be needed to confirm these results.
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Affiliation(s)
- Eric J McGrath
- Carman and Ann Adams Department of Pediatrics, Detroit, MI; Division of Infectious Diseases, Detroit, MI; Children's Hospital of Michigan, Detroit, MI; Wayne State University School of Medicine, Detroit, MI.
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240
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Abstract
Fever is one of the most common reasons for a visit to the primary care provider or the emergency department. Traditionally, clinicians have used various risk-stratification strategies to identify serious bacterial infections (SBI) without an obvious source in febrile children, because missed bacterial infections in such children can result in meningitis, sepsis, and death; therefore, early and accurate identification of SBIs is critical. Infants aged less than 60 to 90 days are at greatest risk of SBI. The epidemiology of SBI continues to evolve, especially after the successful introduction of conjugate vaccines against Streptococcus pneumoniae and Haemophilus influenzae.
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Affiliation(s)
- Rajan Arora
- Division of Emergency Medicine, Carman and Ann Adam Department of Pediatrics, Children's Hospital of Michigan, Wayne State University School of Medicine, 3901 Beaubien Boulevard, Detroit, MI 48201, USA
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241
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Abstract
Influenza viruses cause recurring epidemic outbreaks every year associated with high morbidity and mortality. Despite extensive research and surveillance efforts to control influenza outbreaks, the primary mitigation treatment for influenza is the development of yearly vaccine mixes targeted for the most prevalent virus strains. Consequently, the focus of many detection technologies has evolved toward accurate identification of subtype and understanding the evolution and molecular determinants of novel and pathogenic forms of influenza. The recent availability of potential antiviral treatments are only effective if rapid and accurate diagnostic tests for influenza epidemic management are available; thus, early detection of influenza infection is still important for prevention, containment, patient management, and infection control. This review discusses the current and emerging technologies for detection and strain identification of influenza virus and their specific gene targets, as well as their implications in patient management.
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Affiliation(s)
- Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, U. S. Naval Research Laboratory, 4555 Overlook Avenue, S. W., Code 6900, Washington, DC, 20375, USA
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242
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Community-acquired respiratory viral infections in lung transplant recipients. Curr Opin Infect Dis 2013; 26:302-8. [DOI: 10.1097/qco.0b013e3283630e85] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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243
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Roskos K, Hickerson AI, Lu HW, Ferguson TM, Shinde DN, Klaue Y, Niemz A. Simple system for isothermal DNA amplification coupled to lateral flow detection. PLoS One 2013; 8:e69355. [PMID: 23922706 PMCID: PMC3724848 DOI: 10.1371/journal.pone.0069355] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/09/2013] [Indexed: 02/04/2023] Open
Abstract
Infectious disease diagnosis in point-of-care settings can be greatly improved through integrated, automated nucleic acid testing devices. We have developed an early prototype for a low-cost system which executes isothermal DNA amplification coupled to nucleic acid lateral flow (NALF) detection in a mesofluidic cartridge attached to a portable instrument. Fluid handling inside the cartridge is facilitated through one-way passive valves, flexible pouches, and electrolysis-driven pumps, which promotes a compact and inexpensive instrument design. The closed-system disposable prevents workspace amplicon contamination. The cartridge design is based on standard scalable manufacturing techniques such as injection molding. Nucleic acid amplification occurs in a two-layer pouch that enables efficient heat transfer. We have demonstrated as proof of principle the amplification and detection of Mycobacterium tuberculosis (M.tb) genomic DNA in the cartridge, using either Loop Mediated Amplification (LAMP) or the Exponential Amplification Reaction (EXPAR), both coupled to NALF detection. We envision that a refined version of this cartridge, including upstream sample preparation coupled to amplification and detection, will enable fully-automated sample-in to answer-out infectious disease diagnosis in primary care settings of low-resource countries with high disease burden.
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Affiliation(s)
- Kristina Roskos
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Anna I. Hickerson
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Hsiang-Wei Lu
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Tanya M. Ferguson
- Claremont BioSolutions, Upland, California, United States of America
| | - Deepali N. Shinde
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Yvonne Klaue
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
- * E-mail:
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244
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Litwin CM, Bosley JG. Seasonality and prevalence of respiratory pathogens detected by multiplex PCR at a tertiary care medical center. Arch Virol 2013; 159:65-72. [PMID: 23881085 PMCID: PMC7086932 DOI: 10.1007/s00705-013-1794-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/11/2013] [Indexed: 12/25/2022]
Abstract
Respiratory tract infections (RTIs) are a leading cause of mortality and morbidity. Seasonality has been reported for many viruses, including influenza virus, respiratory syncytial virus (RSV), and the recently described human metapneumovirus (hMPV). We hypothesize that the availability of rapid, multiplex PCR diagnostics will provide better clinical care and new insights into the etiology and clinical spectrum of RTIs. We conducted a retrospective analysis of the incidence of respiratory pathogens at a 500-bed adult and 154-bed pediatric hospital tertiary care center. A total of 939 specimens from patients with an age range of 5 days to 91 years (median, 2 years) were tested by a multiplex respiratory pathogen PCR from November 14, 2011 to November 13, 2012. Sixty-five percent of specimens were positive for at least one pathogen. As the age of the patient increased, the positivity rate for the PCR decreased proportionately. Rhinoviruses/enteroviruses (Rhino/Entero) were the most prevalent (34.3 %) followed by RSV (19.2 %) and hMPV (6.2 %). Twelve percent of the positive samples were positive for multiple analytes, with Rhino/Entero and RSV being the most common combination. The peak months were September and May for Rhino/Entero infections, January for RSV and February for coronavirus. hMPV peaked 2 months after RSV, as has been observed recently in other studies. Multiplex PCR provides rapid diagnostic information that can be used to make knowledgeable clinical decisions and potentially reduce the use of antibiotics. Active respiratory PCR surveillance could also predict seasonal respiratory epidemics to allow for adequate planning of additional infection control measures.
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Affiliation(s)
- Christine M Litwin
- Department of Pathology, Medical College of Georgia, Georgia Regents University, 1120 15th St., Augusta, GA, 30912, USA,
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245
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Das AP, Kumar PS, Swain S. Recent advances in biosensor based endotoxin detection. Biosens Bioelectron 2013; 51:62-75. [PMID: 23934306 DOI: 10.1016/j.bios.2013.07.020] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/28/2013] [Accepted: 07/11/2013] [Indexed: 12/20/2022]
Abstract
Endotoxins also referred to as pyrogens are chemically lipopolysaccharides habitually found in food, environment and clinical products of bacterial origin and are unavoidable ubiquitous microbiological contaminants. Pernicious issues of its contamination result in high mortality and severe morbidities. Standard traditional techniques are slow and cumbersome, highlighting the pressing need for evoking agile endotoxin detection system. The early and prompt detection of endotoxin assumes prime importance in health care, pharmacological and biomedical sectors. The unparalleled recognition abilities of LAL biosensors perched with remarkable sensitivity, high stability and reproducibility have bestowed it with persistent reliability and their possible fabrication for commercial applicability. This review paper entails an overview of various trends in current techniques available and other possible alternatives in biosensor based endotoxin detection together with its classification, epidemiological aspects, thrust areas demanding endotoxin control, commercially available detection sensors and a revolutionary unprecedented approach narrating the influence of omics for endotoxin detection.
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Affiliation(s)
- A P Das
- Bioengineering Laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar, India.
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246
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Abstract
Community-acquired pneumonia (CAP) accounts for major morbidity and mortality in the United States. With improved broad-spectrum antibiotics, the implementation of diagnostic studies has declined and most patients do not have an etiologic pathogen of CAP identified. To enhance the appropriate use of antiviral agents and prevent overuse of antibiotics, the successful management of CAP requires rapid and accurate diagnosis of the etiologic agent of CAP. This article provides an overview of the new rapid molecular tests for the diagnosis of influenza, other respiratory viruses, and bacteria compared with nonmolecular tests and how their use for directed therapy can enhance and improve the management of CAP.
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Affiliation(s)
- Charlotte A Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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247
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Duplex molecular assay intended for point-of-care diagnosis of influenza A/B virus infection. J Clin Microbiol 2013; 51:3031-8. [PMID: 23850955 PMCID: PMC3754654 DOI: 10.1128/jcm.00740-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Early diagnosis and management of influenza virus infection directly correlates with the effectiveness in disease control. Current molecular influenza virus tests were designed for use in diagnostic testing facilities, where sophisticated equipment and highly trained technicians are available. A longer turnaround time for the centralized testing than when testing near the sample source could delay the initiation of medical intervention, thereby reducing the efficacy of antiviral treatment. The new assay, the SAMBA (simple amplification-based assay) Flu duplex test, is a dipstick-based molecular assay developed to provide a simple, accurate, and cost-effective solution for the diagnosis of influenza A/B viruses intended for near-patient testing. The test presents an alternative format of influenza virus molecular testing that utilizes isothermal amplification and visual detection of nucleic acid on a test strip. The entire test procedure (extraction, amplification, and detection) is integrated into an enclosed semiautomated system. Analytically, the SAMBA Flu duplex test detects 95 and 85 copies of viral genomes for influenza A and B viruses, respectively, with no cross-reactivity observed against other common respiratory pathogens. The clinical performance was established by blind testing of 328 nasal/throat and nasopharyngeal swab specimens from the United Kingdom and Belgium and comparing the results with the quantitative reverse transcription-PCR method routinely used in two public health laboratories. The SAMBA Flu duplex test showed a clinical sensitivity and specificity of 100% and 97.9% for influenza virus A and 100% and 100% for influenza virus B. The test provides a new technology that could facilitate simple and timely identification of influenza virus infection, potentially resulting in more efficient control measures.
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248
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Comparison of the FilmArray RP, Verigene RV+, and Prodesse ProFLU+/FAST+ multiplex platforms for detection of influenza viruses in clinical samples from the 2011-2012 influenza season in Belgium. J Clin Microbiol 2013; 51:2977-85. [PMID: 23824777 DOI: 10.1128/jcm.00911-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Respiratory tract infections (RTIs) are caused by a plethora of viral and bacterial pathogens. In particular, lower RTIs are a leading cause of hospitalization and mortality. Timely detection of the infecting respiratory pathogens is crucial to optimize treatment and care. In this study, three U.S. Food and Drug Administration-approved molecular multiplex platforms (Prodesse ProFLU+/FAST+, FilmArray RP, and Verigene RV+) were evaluated for influenza virus detection in 171 clinical samples collected during the Belgian 2011-2012 influenza season. Sampling was done using mid-turbinate flocked swabs, and the collected samples were stored in universal transport medium. The amount of viral RNA present in the swab samples ranged between 3.07 and 8.82 log10 copies/ml. Sixty samples were concordant influenza A virus positive, and 8 samples were found to be concordant influenza B virus positive. Other respiratory viruses that were detected included human rhinovirus/enterovirus, respiratory syncytial virus, parainfluenza virus type 1, human metapneumovirus, and coronavirus NL63. Twenty-five samples yielded discordant results across the various assays which required further characterization by sequencing. The FilmArray RP and Prodesse ProFLU+/FAST+ assays were convenient to perform with regard to sensitivity, ease of use, and low percentages of invalid results. Although the limit of sensitivity is of utmost importance, many other factors should be taken into account in selecting the most convenient molecular diagnostic assay for the detection of respiratory pathogens in clinical samples.
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249
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Two atypical cases of Kingella kingae invasive infection with concomitant human rhinovirus infection. J Clin Microbiol 2013; 51:3137-9. [PMID: 23784119 DOI: 10.1128/jcm.01134-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We describe two atypical cases of Kingella kingae infection in children diagnosed by PCR, one case involving a soft tissue abscess and one case a femoral Brodie abscess. Both patients had concomitant human rhinovirus infection. K. kingae strains, isolated from an oropharyngeal swab, were characterized by multilocus sequence typing and rtxA sequencing.
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250
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Niemz A, Boyle DS. Nucleic acid testing for tuberculosis at the point-of-care in high-burden countries. Expert Rev Mol Diagn 2013; 12:687-701. [PMID: 23153237 DOI: 10.1586/erm.12.71] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Early diagnosis of tuberculosis (TB) facilitates appropriate treatment initiation and can limit the spread of this highly contagious disease. However, commonly used TB diagnostic methods are slow, often insensitive, cumbersome and inaccessible to most patients in TB endemic countries that lack necessary resources. This review discusses nucleic acid amplification technologies, which are being developed for rapid near patient TB diagnosis, that are in the market or undergoing clinical evaluation. They are based on PCR or isothermal methods and are implemented as manual assays or partially/fully integrated instrument systems, with associated tradeoffs between clinical performance, cost, robustness, quality assurance and usability in remote settings by minimally trained personnel. Unmet needs prevail for the identification of drug-resistant TB and for TB diagnosis in HIV-positive and pediatric patients.
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Affiliation(s)
- Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA.
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