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Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clin Microbiol Rev 2018; 32:32/1/e00042-18. [PMID: 30541871 DOI: 10.1128/cmr.00042-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.
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Kreslake JM, Wahyuningrum Y, Iuliano AD, Storms AD, Lafond KE, Mangiri A, Praptiningsih CY, Safi B, Uyeki TM, Storey JD. The Intersection of Care Seeking and Clinical Capacity for Patients With Highly Pathogenic Avian Influenza A (H5N1) Virus in Indonesia: Knowledge and Treatment Practices of the Public and Physicians. Disaster Med Public Health Prep 2016; 10:838-847. [PMID: 27298195 PMCID: PMC6636322 DOI: 10.1017/dmp.2016.81] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND Indonesia has the highest human mortality from highly pathogenic avian influenza (HPAI) A (H5N1) virus infection in the world. METHODS A survey of households (N=2520) measured treatment sources and beliefs among symptomatic household members. A survey of physicians (N=554) in various types of health care facilities measured knowledge, assessment and testing behaviors, and perceived clinical capacity. RESULTS Households reported confidence in health care system capacity but infrequently sought treatment for potential HPAI H5N1 signs/symptoms. More clinicians were confident in their knowledge of diagnosis and treatment than in the adequacy of related equipment and resources at their facilities. Physicians expressed awareness of the HPAI H5N1 suspect case definition, yet expressed only moderate knowledge in questioning symptomatic patients about exposures. Self-reported likelihood of testing for HPAI H5N1 virus was high after learning of certain exposures. Knowledge of antiviral treatment was moderate, but it was higher among clinicians in puskesmas. Physicians in private outpatient clinics, the most heavily used facilities, reported the lowest confidence in their diagnostic and treatment capabilities. CONCLUSIONS Educational campaigns can encourage recall of possible poultry exposure when patients are experiencing signs/symptoms and can raise awareness of the effectiveness of antivirals to drive people to seek health care. Clinicians may benefit from training regarding exposure assessment and referral procedures, particularly in private clinics. (Disaster Med Public Health Preparedness. 2016;10:838-847).
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Affiliation(s)
- Jennifer M Kreslake
- 1Johns Hopkins Bloomberg School of Public Health,Center for Communication Programs,Baltimore,Maryland
| | - Yunita Wahyuningrum
- 1Johns Hopkins Bloomberg School of Public Health,Center for Communication Programs,Baltimore,Maryland
| | - Angela D Iuliano
- 2Influenza Division,Centers for Disease Control and Prevention.Atlanta,Georgia
| | - Aaron D Storms
- 2Influenza Division,Centers for Disease Control and Prevention.Atlanta,Georgia
| | - Kathryn E Lafond
- 2Influenza Division,Centers for Disease Control and Prevention.Atlanta,Georgia
| | - Amalya Mangiri
- 2Influenza Division,Centers for Disease Control and Prevention.Atlanta,Georgia
| | | | - Basil Safi
- 1Johns Hopkins Bloomberg School of Public Health,Center for Communication Programs,Baltimore,Maryland
| | - Timothy M Uyeki
- 2Influenza Division,Centers for Disease Control and Prevention.Atlanta,Georgia
| | - J Douglas Storey
- 1Johns Hopkins Bloomberg School of Public Health,Center for Communication Programs,Baltimore,Maryland
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Mangiri A, Iuliano AD, Wahyuningrum Y, Praptiningsih CY, Lafond KE, Storms AD, Samaan G, Ariawan I, Soeharno N, Kreslake JM, Storey JD, Uyeki TM. Physician's knowledge, attitudes, and practices regarding seasonal influenza, pandemic influenza, and highly pathogenic avian influenza A (H5N1) virus infections of humans in Indonesia. Influenza Other Respir Viruses 2016; 11:93-99. [PMID: 27554302 PMCID: PMC5155649 DOI: 10.1111/irv.12428] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2016] [Indexed: 01/13/2023] Open
Abstract
Indonesia has reported highest number of fatal human cases of highly pathogenic avian influenza (HPAI) A (H5N1) virus infection worldwide since 2005. There are limited data available on seasonal and pandemic influenza in Indonesia. During 2012, we conducted a survey of clinicians in two districts in western Java, Indonesia, to assess knowledge, attitudes, and practices (KAP) of clinical diagnosis, testing, and treatment of patients with seasonal influenza, pandemic influenza, or HPAI H5N1 virus infections. Overall, a very low percentage of physician participants reported ever diagnosing hospitalized patients with seasonal, pandemic, or HPAI H5N1 influenza. Use of influenza testing was low in outpatients and hospitalized patients, and use of antiviral treatment was very low for clinically diagnosed influenza patients. Further research is needed to explore health system barriers for influenza diagnostic testing and availability of antivirals for treatment of influenza in Indonesia.
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Affiliation(s)
- Amalya Mangiri
- US Centers for Disease Control and Prevention, Jakarta, Indonesia
| | - A Danielle Iuliano
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Yunita Wahyuningrum
- Johns Hopkins Center for Communication Programs, Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Kathryn E Lafond
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Aaron D Storms
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA.,Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Gina Samaan
- US Centers for Disease Control and Prevention, Jakarta, Indonesia
| | - Iwan Ariawan
- Center for Health Research, Universitas Indonesia, Jakarta, Indonesia
| | - Nugroho Soeharno
- Center for Health Research, Universitas Indonesia, Jakarta, Indonesia
| | - Jennifer M Kreslake
- Johns Hopkins Center for Communication Programs, Bloomberg School of Public Health, Baltimore, MD, USA
| | - J Douglas Storey
- Johns Hopkins Center for Communication Programs, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Timothy M Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
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