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Sofia de Olazarra A, Chen FE, Wang TH, Wang SX. Rapid, Point-of-Care Host-Based Gene Expression Diagnostics Using Giant Magnetoresistive Biosensors. ACS Sens 2023; 8:2780-2790. [PMID: 37368357 DOI: 10.1021/acssensors.3c00696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Host-based gene expression analysis is a promising tool for a broad range of clinical applications, including rapid infectious disease diagnostics and real-time disease monitoring. However, the complex instrumentation requirements and slow turnaround-times associated with traditional gene expression analysis methods have hampered their widespread adoption at the point-of-care (POC). To overcome these challenges, we have developed an automated and portable platform that utilizes polymerase chain reaction (PCR) and giant magnetoresistive (GMR) biosensors to perform rapid multiplexed, targeted gene expression analysis at the POC. As proof-of-concept, we utilized our platform to amplify and measure the expression of four genes (HERC5, HERC6, IFI27, and IFIH1) that were previously shown to be upregulated in hosts infected with influenza viruses. The compact instrument conducted highly automated PCR amplification and GMR detection to measure the expression of the four genes in multiplex, then utilized Bluetooth communication to relay results to users on a smartphone application. To validate the platform, we tested 20 cDNA samples from symptomatic patients that had been previously diagnosed as either influenza-positive or influenza-negative using a RT-PCR virology panel. A non-parametric Mann-Whitney test revealed that day 0 (day of symptom onset) gene expression was significantly different between the two groups (p < 0.0001, n = 20). Hence, we preliminarily demonstrated that our platform could accurately discriminate between symptomatic influenza and non-influenza populations based on host gene expression in ∼30 min. This study not only establishes the potential clinical utility of our proposed assay and device for influenza diagnostics but it also paves the way for broadscale and decentralized implementation of host-based gene expression diagnostics at the POC.
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Affiliation(s)
- Ana Sofia de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94035, United States
| | - Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Shan X Wang
- Department of Electrical Engineering, Stanford University, Stanford, California 94035, United States
- Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
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Jaffe IS, Jaehne AK, Quackenbush E, Ko ER, Rivers EP, McClain MT, Ginsburg GS, Woods CW, Tsalik EL. Comparing the Diagnostic Accuracy of Clinician Judgment to a Novel Host Response Diagnostic for Acute Respiratory Illness. Open Forum Infect Dis 2021; 8:ofab564. [PMID: 34888402 DOI: 10.1093/ofid/ofab564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 11/12/2022] Open
Abstract
Background Difficulty discriminating bacterial from viral infections drives antibacterial misuse. Host gene expression tests discriminate bacterial and viral etiologies, but their clinical utility has not been evaluated. Methods Host gene expression and procalcitonin levels were measured in 582 emergency department participants with suspected infection. We also recorded clinician diagnosis and clinician-recommended treatment. These 4 diagnostic strategies were compared with clinical adjudication as the reference. To estimate the clinical impact of host gene expression, we calculated the change in overall Net Benefit (∆NB; the difference in Net Benefit comparing 1 diagnostic strategy with a reference) across a range of prevalence estimates while factoring in the clinical significance of false-positive and -negative errors. Results Gene expression correctly classified bacterial, viral, or noninfectious illness in 74.1% of subjects, similar to the other strategies. Clinical diagnosis and clinician-recommended treatment revealed a bias toward overdiagnosis of bacterial infection resulting in high sensitivity (92.6% and 94.5%, respectively) but poor specificity (67.2% and 58.8%, respectively), resulting in a 33.3% rate of inappropriate antibacterial use. Gene expression offered a more balanced sensitivity (79.0%) and specificity (80.7%), which corresponded to a statistically significant improvement in average weighted accuracy (79.9% vs 71.5% for procalcitonin and 76.3% for clinician-recommended treatment; P<.0001 for both). Consequently, host gene expression had greater Net Benefit in diagnosing bacterial infection than clinician-recommended treatment (∆NB=6.4%) and procalcitonin (∆NB=17.4%). Conclusions Host gene expression-based tests to distinguish bacterial and viral infection can facilitate appropriate treatment, improving patient outcomes and mitigating the antibacterial resistance crisis.
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Affiliation(s)
- Ian S Jaffe
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Anja K Jaehne
- Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, Michigan, USA
| | - Eugenia Quackenbush
- Department of Emergency Medicine, University of North Carolina Medical Center, Chapel Hill, North Carolina, USA
| | - Emily R Ko
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Emanuel P Rivers
- Department of Emergency Medicine, Henry Ford Hospital, Wayne State University, Detroit, Michigan, USA
| | - Micah T McClain
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Medical Service, Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Geoffrey S Ginsburg
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christopher W Woods
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Medical Service, Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
| | - Ephraim L Tsalik
- Duke Center for Applied Genomics & Precision Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA.,Emergency Medicine Service, Durham Veterans Affairs Health Care System, Durham, North Carolina, USA
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Chen Y, Mah MG, Low JG, Ooi EE, Su YC, Moorthy M, Smith GJ, Linster M. Etiology of febrile respiratory infections in the general adult population in Singapore, 2007-2013. Heliyon 2021; 7:e06329. [PMID: 33665466 PMCID: PMC7907478 DOI: 10.1016/j.heliyon.2021.e06329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/11/2021] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Pathogens that cause upper respiratory infections are numerous and specific preventive and therapeutic strategies are scarce. In order to ascertain the etiological agents resulting in upper respiratory tract infections (URTI) in adults in Singapore, nasal swab samples were collected from 2057 patients presenting with fever at primary healthcare clinics in Singapore from December 2007 to February 2013. Samples were tested using the Luminex NxTAG Respiratory Pathogen Panel that includes 22 respiratory pathogen targets. Patient-reported symptoms and vital signs were recorded and full blood and differential counts taken. Pathogens were detected in the following order of frequency: influenza viruses, rhino-/enteroviruses, coronaviruses, parainfluenza viruses, pneumoviruses, adenovirus, bocavirus and C. pneumoniae. Fifteen virus species were detected as part of coinfections, in which rhinoviruses were the most commonly observed pathogen. Our results suggest that influenza viruses are the main etiological agents, but multiple other respiratory viruses contribute to the total burden of URTI in adults in Singapore.
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Affiliation(s)
- Yihui Chen
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Marcus G. Mah
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Jenny G.H. Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Department of Infectious Diseases, Singapore General Hospital, Singapore 169856, Singapore
| | - Eng Eong Ooi
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Yvonne C.F. Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Mahesh Moorthy
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Gavin J.D. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
- Duke Global Health Institute, Duke University, Durham, North Carolina 27708, USA
- Corresponding author.
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
- Corresponding author.
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McClain MT, Constantine FJ, Nicholson BP, Nichols M, Burke TW, Henao R, Jones DC, Hudson LL, Jaggers LB, Veldman T, Mazur A, Park LP, Suchindran S, Tsalik EL, Ginsburg GS, Woods CW. A blood-based host gene expression assay for early detection of respiratory viral infection: an index-cluster prospective cohort study. THE LANCET. INFECTIOUS DISEASES 2020; 21:396-404. [PMID: 32979932 PMCID: PMC7515566 DOI: 10.1016/s1473-3099(20)30486-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 05/07/2020] [Accepted: 05/14/2020] [Indexed: 01/31/2023]
Abstract
Background Early and accurate identification of individuals with viral infections is crucial for clinical management and public health interventions. We aimed to assess the ability of transcriptomic biomarkers to identify naturally acquired respiratory viral infection before typical symptoms are present. Methods In this index-cluster study, we prospectively recruited a cohort of undergraduate students (aged 18–25 years) at Duke University (Durham, NC, USA) over a period of 5 academic years. To identify index cases, we monitored students for the entire academic year, for the presence and severity of eight symptoms of respiratory tract infection using a daily web-based survey, with symptoms rated on a scale of 0–4. Index cases were defined as individuals who reported a 6-point increase in cumulative daily symptom score. Suspected index cases were visited by study staff to confirm the presence of reported symptoms of illness and to collect biospecimen samples. We then identified clusters of close contacts of index cases (ie, individuals who lived in close proximity to index cases, close friends, and partners) who were presumed to be at increased risk of developing symptomatic respiratory tract infection while under observation. We monitored each close contact for 5 days for symptoms and viral shedding and measured transcriptomic responses at each timepoint each day using a blood-based 36-gene RT-PCR assay. Findings Between Sept 1, 2009, and April 10, 2015, we enrolled 1465 participants. Of 264 index cases with respiratory tract infection symptoms, 150 (57%) had a viral cause confirmed by RT-PCR. Of their 555 close contacts, 106 (19%) developed symptomatic respiratory tract infection with a proven viral cause during the observation window, of whom 60 (57%) had the same virus as their associated index case. Nine viruses were detected in total. The transcriptomic assay accurately predicted viral infection at the time of maximum symptom severity (mean area under the receiver operating characteristic curve [AUROC] 0·94 [95% CI 0·92–0·96]), as well as at 1 day (0·87 [95% CI 0·84–0·90]), 2 days (0·85 [0·82–0·88]), and 3 days (0·74 [0·71–0·77]) before peak illness, when symptoms were minimal or absent and 22 (62%) of 35 individuals, 25 (69%) of 36 individuals, and 24 (82%) of 29 individuals, respectively, had no detectable viral shedding. Interpretation Transcriptional biomarkers accurately predict and diagnose infection across diverse viral causes and stages of disease and thus might prove useful for guiding the administration of early effective therapy, quarantine decisions, and other clinical and public health interventions in the setting of endemic and pandemic infectious diseases. Funding US Defense Advanced Research Projects Agency.
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Affiliation(s)
- Micah T McClain
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA.
| | - Florica J Constantine
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Marshall Nichols
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | | | - Lori L Hudson
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - L Brett Jaggers
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Timothy Veldman
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Anna Mazur
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Lawrence P Park
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
| | - Sunil Suchindran
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University Medical Center, Durham, NC, USA; Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA; Durham VA Medical Center, Durham, NC, USA
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Nguyen TTK, Ngo TT, Tran PM, Pham TTT, Vu HTT, Nguyen NTH, Thwaites G, Virtala AK, Vapalahti O, Baker S, Le Van T. Respiratory viruses in individuals with a high frequency of animal exposure in southern and highland Vietnam. J Med Virol 2020; 92:971-981. [PMID: 31769525 PMCID: PMC7228379 DOI: 10.1002/jmv.25640] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/22/2019] [Indexed: 12/23/2022]
Abstract
Active surveillance for zoonotic respiratory viruses is essential to inform the development of appropriate interventions and outbreak responses. Here we target individuals with a high frequency of animal exposure in Vietnam. Three-year community-based surveillance was conducted in Vietnam during 2013-2016. We enrolled a total of 581 individuals (animal-raising farmers, slaughterers, animal-health workers, and rat traders), and utilized reverse transcription-polymerase chain reaction to detect 15 common respiratory viruses in pooled nasal-throat swabs collected at baseline or acute respiratory disease episodes. A respiratory virus was detected in 7.9% (58 of 732) of baseline samples, and 17.7% (136 of 770) of disease episode samples (P < .001), with enteroviruses (EVs), rhinoviruses and influenza A virus being the predominant viruses detected. There were temporal and spatial fluctuations in the frequencies of the detected viruses over the study period, for example, EVs and influenza A viruses were more often detected during rainy seasons. We reported the detection of common respiratory viruses in individuals with a high frequency of animal exposure in Vietnam, an emerging infectious disease hotspot. The results show the value of baseline/control sampling in delineating the causative relationships and have revealed important insights into the ecological aspects of EVs, rhinoviruses and influenza A and their contributions to the burden posed by respiratory infections in Vietnam.
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Affiliation(s)
- Tu Thi Kha Nguyen
- Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
- Dong Thap Provincial Center for Disease ControlDong Thap ProvinceVietnam
| | - Tue Tri Ngo
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
| | - Phuc My Tran
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
| | | | - Hang Thi Ty Vu
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
| | | | - Guy Thwaites
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
- Centre for Tropical Medicine and Global HealthOxford UniversityOxfordUnited Kingdom
| | - Anna‐Maija K. Virtala
- Department of Veterinary Biosciences, Faculty of Veterinary MedicineUniversity of HelsinkiHelsinkiFinland
| | - Olli Vapalahti
- Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of Veterinary Biosciences, Faculty of Veterinary MedicineUniversity of HelsinkiHelsinkiFinland
- Department of Virology and ImmunologyHUSLAB, Helsinki University HospitalHelsinkiFinland
| | - Stephen Baker
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
- Centre for Tropical Medicine and Global HealthOxford UniversityOxfordUnited Kingdom
- Department of MedicineUniversity of CambridgeCambridgeUnited Kingdom
| | - Tan Le Van
- Oxford University Clinical Research UnitHo Chi Minh CityVietnam
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Muthanna A, Salim HS, Hamat RA, Shamsuddin NH, Zakariah SZ. Clinical Screening Tools to Diagnose Group A Streptococcal Pharyngotonsillitis in Primary Care Clinics to Improve Prescribing Habits. Malays J Med Sci 2018; 25:6-21. [PMID: 30914875 PMCID: PMC6422577 DOI: 10.21315/mjms2018.25.6.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 07/30/2018] [Indexed: 12/02/2022] Open
Abstract
This review highlights the clinical scoring tools used for the management of acute pharyngotonsillitis in primary care clinics. It will include the prevalence of group A pharyngotonsillitis among children and adults worldwide and the selective tests employed for diagnosing group A streptococcal pharyngotonsillitis. Pharyngotonsillitis is one of the common reasons for visits to primary care clinics worldwide, and physicians tend to prescribe antibiotics according to the clinical symptoms, which leads to overprescribing antibiotics. This in turn may lead to serious health impacts and severe reactions and may promote antibiotic resistance. These significantly add on to the health care costs. The available information from health organisations and previous studies has indicated the need to manage the diagnosis of pharyngotonsillitis to improve prescribing habits in primary care clinics.
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Affiliation(s)
- Abdulrahman Muthanna
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Hani Syahida Salim
- Department of Family Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Rukman Awang Hamat
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Nurainul Hana Shamsuddin
- Department of Family Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Zulaikha Zakariah
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Al-Tawfiq JA, Benkouiten S, Memish ZA. A systematic review of emerging respiratory viruses at the Hajj and possible coinfection with Streptococcus pneumoniae. Travel Med Infect Dis 2018; 23:6-13. [PMID: 29673810 PMCID: PMC7110954 DOI: 10.1016/j.tmaid.2018.04.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/10/2018] [Accepted: 04/11/2018] [Indexed: 12/15/2022]
Abstract
Background The annual Hajj to the Kingdom of Saudi Arabia attracts millions of pilgrims from around the world. International health community's attention goes towards this mass gathering and the possibility of the development of any respiratory tract infections due to the high risk of acquisition of respiratory viruses. Method We searched MEDLINE/PubMed and Scopus databases for relevant papers describing the prevalence of respiratory viruses among Hajj pilgrims. Results The retrieved articles were summarized based on the methodology of testing for these viruses. A total of 31 studies were included in the quantitative/qualitative analyses. The main methods used for the diagnosis of most common respiratory viruses were polymerase chain reaction (PCR), culture and enzyme-linked immunosorbent assay (ELISA). Influenza, rhinovirus and parainfluenza were the most common viruses detected among pilgrims. Coronaviruses other than MERS-CoV were also detected among pilgrims. The acquisition of MERS-CoV remains very limited and systematic screening of pilgrims showed no infections. Conclusions Well conducted multinational follow-up studies using the same methodology of testing are necessary for accurate surveillance of respiratory viral infections among Hajj pilgrims. Post-Hajj cohort studies would further evaluate the impact of the Hajj on the acquisition of respiratory viruses.
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Affiliation(s)
- Jaffar A Al-Tawfiq
- Specialty Internal Medicine Unit, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Indiana University School of Medicine, Indianapolis, IN 46202, USA; Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Samir Benkouiten
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France; Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Ziad A Memish
- Department of Medicine and Research, Prince Mohammed Bin Abdulaziz Hospital, Ministry of Health, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Rollins School of Public Health, Emory University, Atlanta, GA, United States.
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Burke TW, Henao R, Soderblom E, Tsalik EL, Thompson JW, McClain MT, Nichols M, Nicholson BP, Veldman T, Lucas JE, Moseley MA, Turner RB, Lambkin-Williams R, Hero AO, Woods CW, Ginsburg GS. Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection. EBioMedicine 2017; 17:172-181. [PMID: 28238698 PMCID: PMC5360578 DOI: 10.1016/j.ebiom.2017.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 12/09/2022] Open
Abstract
Infection of respiratory mucosa with viral pathogens triggers complex immunologic events in the affected host. We sought to characterize this response through proteomic analysis of nasopharyngeal lavage in human subjects experimentally challenged with influenza A/H3N2 or human rhinovirus, and to develop targeted assays measuring peptides involved in this host response allowing classification of acute respiratory virus infection. Unbiased proteomic discovery analysis identified 3285 peptides corresponding to 438 unique proteins, and revealed that infection with H3N2 induces significant alterations in protein expression. These include proteins involved in acute inflammatory response, innate immune response, and the complement cascade. These data provide insights into the nature of the biological response to viral infection of the upper respiratory tract, and the proteins that are dysregulated by viral infection form the basis of signature that accurately classifies the infected state. Verification of this signature using targeted mass spectrometry in independent cohorts of subjects challenged with influenza or rhinovirus demonstrates that it performs with high accuracy (0.8623 AUROC, 75% TPR, 97.46% TNR). With further development as a clinical diagnostic, this signature may have utility in rapid screening for emerging infections, avoidance of inappropriate antibacterial therapy, and more rapid implementation of appropriate therapeutic and public health strategies.
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Affiliation(s)
- Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Erik Soderblom
- Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27708, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA; Durham Veteran's Affairs Medical Center, Durham, NC 27705, USA; Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27708, USA
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA; Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA; Section for Infectious Diseases, Medicine Service, Durham Veteran's Affairs Medical Center, Durham, NC 27705, USA
| | - Marshall Nichols
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA
| | | | - Timothy Veldman
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA
| | - Joseph E Lucas
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - M Arthur Moseley
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA; Proteomics and Metabolomics Shared Resource, Duke University Medical Center, Durham, NC 27708, USA
| | - Ronald B Turner
- School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | | | - Alfred O Hero
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA; Division of Infectious Diseases and International Health, Department of Medicine, Duke University, Durham, NC 27710, USA; Section for Infectious Diseases, Medicine Service, Durham Veteran's Affairs Medical Center, Durham, NC 27705, USA.
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27708, USA.
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Pan DST, Huang JH, Lee MHM, Yu Y, Chen MIC, Goh EH, Jiang L, Chong JWC, Leo YS, Lee TH, Wong CS, Loh VWK, Poh AZ, Tham TY, Wong WM, Lim FS. Knowledge, attitudes and practices towards antibiotic use in upper respiratory tract infections among patients seeking primary health care in Singapore. BMC FAMILY PRACTICE 2016; 17:148. [PMID: 27809770 PMCID: PMC5094024 DOI: 10.1186/s12875-016-0547-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 10/21/2016] [Indexed: 11/10/2022]
Abstract
Background Patients’ expectations can influence antibiotic prescription by primary healthcare physicians. We assessed knowledge, attitude and practices towards antibiotic use for upper respiratory tract infections (URTIs), and whether knowledge is associated with increased expectations for antibiotics among patients visiting primary healthcare services in Singapore. Methods Data was collected through a cross-sectional interviewer-assisted survey of patients aged ≥21 years waiting to see primary healthcare practitioners for one or more symptoms suggestive of URTI (cough, sore throat, runny nose or blocked nose) for 7 days or less, covering the demographics, presenting symptoms, knowledge, attitudes, beliefs and practices of URTI and associated antibiotic use. Univariate and multivariate logistic regression was used to assess independent factors associated with patients’ expectations for antibiotics. Results Nine hundred fourteen out of 987 eligible patients consulting 35 doctors were recruited from 24 private sector primary care clinics in Singapore. A third (307/907) expected antibiotics, of which a substantial proportion would ask the doctor for antibiotics (121/304, 40 %) and/or see another doctor (31/304, 10 %) if antibiotics were not prescribed. The majority agreed “antibiotics are effective against viruses” (715/914, 78 %) and that “antibiotics cure URTI faster” (594/912, 65 %). Inappropriate antibiotic practices include “keeping antibiotics stock at home” (125/913, 12 %), “taking leftover antibiotics” (114/913, 14 %) and giving antibiotics to family members (62/913, 7 %). On multivariate regression, the following factors were independently associated with wanting antibiotics (odds ratio; 95 % confidence interval): Malay ethnicity (1.67; 1.00–2.79), living in private housing (1.69; 1.13–2.51), presence of sore throat (1.50; 1.07–2.10) or fever (1.46; 1.01–2.12), perception that illness is serious (1.70; 1.27–2.27), belief that antibiotics cure URTI faster (5.35; 3.76–7.62) and not knowing URTI resolves on its own (2.18; 1.08–2.06), while post-secondary education (0.67; 0.48–0.94) was inversely associated. Those with lower educational levels were significantly more likely to have multiple misconceptions about antibiotics. Conclusion Majority of patients seeking primary health care in Singapore are misinformed about the role of antibiotics in URTI. Agreeing with the statement that antibiotics cure URTI faster was most strongly associated with wanting antibiotics. Those with higher educational levels were less likely to want antibiotics, while those with lower educational levels more likely to have incorrect knowledge. Electronic supplementary material The online version of this article (doi:10.1186/s12875-016-0547-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Darius Shaw Teng Pan
- Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 119228, Singapore, Singapore
| | - Joyce Huixin Huang
- Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 119228, Singapore, Singapore
| | - Magdalene Hui Min Lee
- Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 119228, Singapore, Singapore
| | - Yue Yu
- Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 119228, Singapore, Singapore
| | - Mark I-Cheng Chen
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, 12 Science Drive 2, 117549, Singapore, Singapore. .,Institute of Infectious Diseases & Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, 308433, Singapore, Singapore.
| | - Ee Hui Goh
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, 12 Science Drive 2, 117549, Singapore, Singapore
| | - Lili Jiang
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, 12 Science Drive 2, 117549, Singapore, Singapore
| | - Joash Wen Chen Chong
- Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, 12 Science Drive 2, 117549, Singapore, Singapore
| | - Yee Sin Leo
- Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 119228, Singapore, Singapore.,Saw Swee Hock School of Public Health, National University Health System, National University of Singapore, 12 Science Drive 2, 117549, Singapore, Singapore.,Institute of Infectious Diseases & Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, 308433, Singapore, Singapore.,Lee Kong Chian School of Medicine, Nan Yang Technological University, 308232, Singapore, Singapore
| | - Tau Hong Lee
- Institute of Infectious Diseases & Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, 308433, Singapore, Singapore
| | - Chia Siong Wong
- Institute of Infectious Diseases & Epidemiology, Communicable Disease Centre, Tan Tock Seng Hospital, 308433, Singapore, Singapore
| | - Victor Weng Keong Loh
- Division of Family Medicine, Department of Medicine, University Medicine Cluster, National University Hospital System, 119228, Singapore, Singapore
| | | | - Tat Yean Tham
- Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 119228, Singapore, Singapore.,Division of Family Medicine, Department of Medicine, University Medicine Cluster, National University Hospital System, 119228, Singapore, Singapore.,Frontier Healthcare group, 400305, Singapore, Singapore
| | - Wei Mon Wong
- Division of Family Medicine, Department of Medicine, University Medicine Cluster, National University Hospital System, 119228, Singapore, Singapore.,Division of Primary Care, Raffles Medical Group, 188770, Singapore, Singapore.,Duke NUS Graduate Medical School, National University of Singapore, 169857, Singapore, Singapore
| | - Fong Seng Lim
- Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 119228, Singapore, Singapore.,Division of Family Medicine, Department of Medicine, University Medicine Cluster, National University Hospital System, 119228, Singapore, Singapore
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10
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Ho ZJM, Zhao X, Cook AR, Loh JP, Ng SH, Tan BH, Lee VJ. Clinical differences between respiratory viral and bacterial mono- and dual pathogen detected among Singapore military servicemen with febrile respiratory illness. Influenza Other Respir Viruses 2016; 9:200-8. [PMID: 25827870 PMCID: PMC4474496 DOI: 10.1111/irv.12312] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2015] [Indexed: 01/04/2023] Open
Abstract
Background Although it is known that febrile respiratory illnesses (FRI) may be caused by multiple respiratory pathogens, there are no population-level studies describing its impact on clinical disease. Methods Between May 2009 and October 2012, 7733 FRI patients and controls in the Singapore military had clinical data and nasal wash samples collected prospectively and sent for PCR testing. Patients with one pathogen detected (mono-pathogen) were compared with those with two pathogens (dual pathogen) for differences in basic demographics and clinical presentation. Results In total, 45.8% had one pathogen detected, 20.2% had two pathogens detected, 30.9% had no pathogens detected, and 3.1% had more than two pathogens. Multiple pathogens were associated with recruits, those with asthma and non-smokers. Influenza A (80.0%), influenza B (73.0%) and mycoplasma (70.6%) were most commonly associated with mono-infections, while adenovirus was most commonly associated with dual infections (62.9%). Influenza A paired with S. pneumoniae had higher proportions of chills and rigors than their respective mono-pathogens (P = 0.03, P = 0.009). H. influenzae paired with either enterovirus or parainfluenzae had higher proportions of cough with phlegm than their respective mono-pathogens. Although there were observed differences in mean proportions of body temperature, nasal symptoms, sore throat, body aches and joint pains between viral and bacterial mono-pathogens, there were few differences between distinct dual-pathogen pairs and their respective mono-pathogen counterparts. Conclusion A substantial number of FRI patients have multiple pathogens detected. Observed clinical differences between patients of dual pathogen and mono-pathogen indicate the likely presence of complex microbial interactions between the various pathogens.
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Affiliation(s)
| | - Xiahong Zhao
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Alex R Cook
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | | | | | | | - Vernon J Lee
- HQ Medical Corps, Singapore Armed Forces, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore
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11
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Linel P, Wu S, Deng N, Wu H. Dynamic transcriptional signatures and network responses for clinical symptoms in influenza-infected human subjects using systems biology approaches. J Pharmacokinet Pharmacodyn 2015; 41:509-21. [PMID: 25015847 DOI: 10.1007/s10928-014-9365-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/14/2014] [Indexed: 01/10/2023]
Abstract
Recent studies demonstrate that human blood transcriptional signatures may be used to support diagnosis and clinical decisions for acute respiratory viral infections such as influenza. In this article, we propose to use a newly developed systems biology approach for time course gene expression data to identify significant dynamically response genes and dynamic gene network responses to viral infection. We illustrate the methodological pipeline by reanalyzing the time course gene expression data from a study with healthy human subjects challenged by live influenza virus. We observed clear differences in the number of significant dynamic response genes (DRGs) between the symptomatic and asymptomatic subjects and also identified DRG signatures for symptomatic subjects with influenza infection. The 505 common DRGs shared by the symptomatic subjects have high consistency with the signature genes for predicting viral infection identified in previous works. The temporal response patterns and network response features were carefully analyzed and investigated.
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12
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Tsalik EL, McClain M, Zaas AK. Moving toward prime time: host signatures for diagnosis of respiratory infections. J Infect Dis 2015; 212:173-5. [PMID: 25637349 DOI: 10.1093/infdis/jiv032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 01/13/2015] [Indexed: 01/12/2023] Open
Affiliation(s)
- Ephraim L Tsalik
- Institute for Genome Sciences and Precision Medicine, Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Micah McClain
- Institute for Genome Sciences and Precision Medicine, Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Aimee K Zaas
- Institute for Genome Sciences and Precision Medicine, Division of Infectious Diseases and International Health, Department of Medicine, Duke University Medical Center, Durham, North Carolina
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13
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Zaas AK, Garner BH, Tsalik EL, Burke T, Woods CW, Ginsburg GS. The current epidemiology and clinical decisions surrounding acute respiratory infections. Trends Mol Med 2014; 20:579-88. [PMID: 25201713 DOI: 10.1016/j.molmed.2014.08.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/05/2014] [Accepted: 08/06/2014] [Indexed: 12/15/2022]
Abstract
Acute respiratory infection (ARI) is a common diagnosis in outpatient and emergent care settings. Currently available diagnostics are limited, creating uncertainty in the use of antibacterial, antiviral, or supportive care. Up to 72% of ambulatory care patients with ARI are treated with an antibacterial, despite only a small fraction actually needing one. Antibiotic overuse is not restricted to ambulatory care: ARI accounts for approximately 5 million emergency department (ED) visits annually in the USA, where 52-61% of such patients receive antibiotics. Thus, an accurate test for the presence or absence of viral or bacterial infection is needed. In this review, we focus on recent research showing that the host-response (genomic, proteomic, or miRNA) can accomplish this task.
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Affiliation(s)
- Aimee K Zaas
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA; Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
| | - Bronwen H Garner
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Ephraim L Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA; Department of Medicine, Duke University School of Medicine, Durham, NC, USA; Durham Veterans Affairs Medical Center, Durham, NC, USA
| | - Thomas Burke
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA; Department of Medicine, Duke University School of Medicine, Durham, NC, USA; Durham Veterans Affairs Medical Center, Durham, NC, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
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14
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Teng CL. Antibiotic prescribing for upper respiratory tract infections in the Asia-Pacific region: A brief review. MALAYSIAN FAMILY PHYSICIAN : THE OFFICIAL JOURNAL OF THE ACADEMY OF FAMILY PHYSICIANS OF MALAYSIA 2014; 9:18-25. [PMID: 25893067 PMCID: PMC4399404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This review highlights the high prevalence of antibiotic use for upper respiratory tract infections (URTIs) in a larger part of the Asia-Pacific region. Since URTIs are one of the common reasons for primary care consultations in this region, inappropriate use of antibiotic in both quantity and drug choice has greatly influenced the development of antibiotic resistance. Notwithstanding the paucity of Asia-Pacific data on the above issues, the available information suggests urgent actions needed to be taken to promote judicious antibiotic use at the point-of-care through a multi-pronged approach targeting the patients/consumers (or parents), healthcare providers and health care systems.
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Affiliation(s)
- CL Teng
- Department of Family Medicine, International Medical University
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15
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Tan XQ, Zhao X, Lee VJ, Loh JP, Tan BH, Koh WHV, Ng SH, Chen MIC, Cook AR. Respiratory viral pathogens among Singapore military servicemen 2009-2012: epidemiology and clinical characteristics. BMC Infect Dis 2014; 14:204. [PMID: 24735158 PMCID: PMC4006965 DOI: 10.1186/1471-2334-14-204] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 04/08/2014] [Indexed: 11/25/2022] Open
Abstract
Background Few studies have comprehensively described tropical respiratory disease surveillance in military populations. There is also a lack of studies comparing clinical characteristics of the non-influenza pathogens with influenza and amongst themselves. Methods From May 2009 through October 2012, 7733 consenting cases of febrile respiratory illness (FRI) (temperature [greater than or equal to]37.5degreesC with cough or sorethroat) and controls in the Singapore military had clinical data and nasal washes collected prospectively. Nasal washes underwent multiplex PCR, and the analysis was limited to viral mono-infections. Results 49% of cases tested positive for at least one virus, of whom 10% had multiple infections. 53% of the FRI cases fulfilled the definition of influenza-like illness (ILI), of whom 52% were positive for at least one virus. The most frequent etiologies for mono-infections among FRI cases were Influenza A(H1N1)pdm09 (13%), Influenza B (13%) and coxsackevirus (9%). The sensitivity, specificity, positive predictive value and negative predictive value of ILI for influenza among FRI cases were 72%, 48%, 40% and 69% respectively. On logistic regression, there were marked differences in the prevalence of different symptoms and signs between viruses with fever more prevalent amongst influenza and adenovirus infections than other viruses. Conclusion There are multiple viral etiologies for FRI and ILI with differing clinical symptoms in the Singapore military. Influenza and coxsackevirus were the most common etiology for FRI, while influenza and adenoviruses displayed the most febrile symptoms. Further studies should explore these differences and possible interventions.
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Affiliation(s)
| | | | - Vernon J Lee
- Biodefence Centre, Ministry of Defence, Singapore, Singapore.
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16
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Mohd Fozi K, Kamaliah M. The effect of profiling report on antibiotic prescription for upper respiratory tract infection. MALAYSIAN FAMILY PHYSICIAN : THE OFFICIAL JOURNAL OF THE ACADEMY OF FAMILY PHYSICIANS OF MALAYSIA 2013; 8:26-31. [PMID: 25606278 PMCID: PMC4170469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
INTRODUCTION Upper respiratory tract infection (URTI) is a common encounter in primary care and mostly viral in origin. Despite frequent reminders to primary care providers on judicious use of antibiotics for URTI, the practice is still rampant. METHODS As part of quality improvement initiative, an intervention was designed by distributing a profiling report on individual prescriber's performance in comparison to colleagues on usage of antibiotic for URTI. The data were generated from electronic health record in three public primary care clinics in Malaysia and emailing monthly throughout 2011 to all providers. RESULTS There were 22,328 consultations for URTI in 2010 and 22,756 in 2011 with the incidence rates of URTI among overall consultations of 15.7% and 15.9% respectively. 60 doctors and medical assistants had performed consultations during the 2 year period. Following the intervention in 2011, the prescription rate of antibiotic for URTI is significantly reduced from 33.5% in 2010 to 23.3 % in 2011. Before intervention, individual prescription rate varies from 9.7% to 88.9% and reduced to 4.3% to 50.5% after intervention. CONCLUSION Profiling report is a potential method of changing antibiotic prescribing habit among public primary care providers in Malaysia especially if the baseline adherence was poor and higher variation of prescribing rate.
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17
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Memish ZA, Assiri AM, Hussain R, Alomar I, Stephens G. Detection of respiratory viruses among pilgrims in Saudi Arabia during the time of a declared influenza A(H1N1) pandemic. J Travel Med 2012; 19:15-21. [PMID: 22221807 PMCID: PMC7537650 DOI: 10.1111/j.1708-8305.2011.00575.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND The objectives of this study were to determine whether pilgrim attendance at the Hajj was associated with an increased risk of acquiring influenza, and other respiratory viruses, and to evaluate the compliance of pilgrims with influenza vaccination and other recommended preventive measures. METHODS A cross-sectional survey was conducted among pilgrims as they arrived at the King Abdulaziz International Airport in Jeddah for the 2009 Hajj and as they departed from the same airport during the week after the Hajj. Nasopharyngeal and throat swabs were tested for 18 respiratory virus types and subtypes using the xTAG Respiratory Viral Panel FAST assay. RESULTS A total of 519 arriving pilgrims and 2,699 departing pilgrims were examined. Their mean age was 49 years and 58% were male. In all, 30% of pilgrims stated that they had received pandemic influenza A(H1N1) vaccine before leaving for the Hajj and 35% of arriving pilgrims reported wearing a face mask. Only 50% of arriving pilgrims were aware of preventive measures such as hand hygiene and wearing a mask. The prevalence of any respiratory-virus infection was 14.5% (12.5% among arriving pilgrims and 14.8% among departing pilgrims). The main viruses detected (both groups combined) were rhinovirus-enterovirus (N = 414, 12.9%), coronaviruses (N = 27, 0.8%), respiratory syncytial virus (N = 8, 0.2%), and influenza A virus (N = 8, 0.2%) including pandemic influenza A(H1N1) (N = 3, 0.1%). The prevalence of pandemic influenza A(H1N1) was 0.2% (N = 1) among arriving pilgrims and 0.1% (N = 2) among departing pilgrims. The prevalence of any respiratory virus infection was lower among those who said they received H1N1 vaccine compared to those who said they did not receive it (11.8% vs 15.6%, respectively, p = 0.009). CONCLUSION We found very low pandemic influenza A(H1N1) prevalence among arriving pilgrims and no evidence that amplification of transmission had occurred among departing pilgrims.
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Affiliation(s)
- Ziad A Memish
- Department of Preventive Medicine, Ministry of Health, Riyadh, Kingdom of Saudi Arabia.
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18
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Memish ZA, Assiri AM, Alshehri M, Hussain R, Alomar I. The prevalance of respiratory viruses among healthcare workers serving pilgrims in Makkah during the 2009 influenza A (H1N1) pandemic. Travel Med Infect Dis 2011; 10:18-24. [PMID: 22197024 PMCID: PMC7106026 DOI: 10.1016/j.tmaid.2011.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Revised: 11/08/2011] [Accepted: 11/23/2011] [Indexed: 11/08/2022]
Abstract
Despite the high risk of acquiring respiratory infections, healthcare workers who treat pilgrims at Hajj have not been studied in previous research on respiratory diseases during Hajj. The objective of this study was to determine the prevalence of different respiratory viruses among healthcare workers who treated pilgrims during Hajj 2009, the year of the influenza A H1N1 pandemic. A cross-sectional study was performed just before and after Hajj (25–29 November, 2009). Nasal and throat swabs were tested for 18 respiratory virus types and subtypes. A total of 184 healthcare workers were examined. Most were men (85%) with an average age of 41 years. Before the Hajj, rates of seasonal influenza vaccination were higher (51%) than rates of pandemic influenza A H1N1 vaccination (22%). After the Hajj, participants reported high rates of maintaining hand hygiene (98%), cough etiquette (89%), and wearing a face mask (90%). Among all the viruses tested, only two were detected: rhinovirus was detected in 12.6% and Coronavirus 229E in 0.6%. Rhinovirus was detected in 21% of those who had respiratory symptoms during Hajj. Influenza A (including H1N1), influenza B. respiratory syncytial virus, other coronaviruses, parainfluenza viruses, human metapneumovirus, adenovirus, and human bocavirus were not detected. The finding of high rates of rhinovirus infection corresponds to their frequent occurrence in adults. None of the participants had influenza A H1N1 2009, possibly because it was also infrequent among the 2009 pilgrims.
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Affiliation(s)
- Ziad A Memish
- Preventive Medicine Directorate, Ministry of Health, & AlFaisal University, Riyadh, Saudi Arabia.
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19
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Lee VJ, Yap J, Cook AR, Tan CH, Loh JP, Koh WH, Lim EAS, Liaw JCW, Chew JSW, Hossain I, Chan KW, Ting PJ, Ng SH, Gao Q, Kelly PM, Chen MI, Tambyah PA, Tan BH. A clinical diagnostic model for predicting influenza among young adult military personnel with febrile respiratory illness in Singapore. PLoS One 2011; 6:e17468. [PMID: 21399686 PMCID: PMC3047544 DOI: 10.1371/journal.pone.0017468] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2010] [Accepted: 01/28/2011] [Indexed: 11/19/2022] Open
Abstract
Introduction Influenza infections present with wide-ranging clinical features. We aim to
compare the differences in presentation between influenza and non-influenza
cases among those with febrile respiratory illness (FRI) to determine
predictors of influenza infection. Methods Personnel with FRI (defined as fever≥37.5°C, with cough or sore
throat) were recruited from the sentinel surveillance system in the
Singapore military. Nasal washes were collected, and tested using the
Resplex II and additional PCR assays for etiological determination.
Interviewer-administered questionnaires collected information on patient
demographics and clinical features. Univariate comparison of the various
parameters was conducted, with statistically significant parameters entered
into a multivariate logistic regression model. The final multivariate model
for influenza versus non-influenza cases was used to build a predictive
probability clinical diagnostic model. Results 821 out of 2858 subjects recruited from 11 May 2009 to 25 Jun 2010 had
influenza, of which 434 (52.9%) had 2009 influenza A (H1N1), 58
(7.1%) seasonal influenza A (H3N2) and 269 (32.8%) influenza
B. Influenza-positive cases were significantly more likely to present with
running nose, chills and rigors, ocular symptoms and higher temperature, and
less likely with sore throat, photophobia, injected pharynx, and
nausea/vomiting. Our clinical diagnostic model had a sensitivity of
65% (95% CI: 58%, 72%), specificity of
69% (95% CI: 62%, 75%), and overall accuracy of
68% (95% CI: 64%, 71%), performing significantly
better than conventional influenza-like illness (ILI) criteria. Conclusions Use of a clinical diagnostic model may help predict influenza better than the
conventional ILI definition among young adults with FRI.
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Affiliation(s)
- Vernon J Lee
- Biodefence Centre, Ministry of Defence, Singapore, Singapore.
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20
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Zaas AK, Chen M, Varkey J, Veldman T, Hero AO, Lucas J, Huang Y, Turner R, Gilbert A, Lambkin-Williams R, Øien NC, Nicholson B, Kingsmore S, Carin L, Woods CW, Ginsburg GS. Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans. Cell Host Microbe 2009; 6:207-17. [PMID: 19664979 DOI: 10.1016/j.chom.2009.07.006] [Citation(s) in RCA: 291] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 05/27/2009] [Accepted: 07/22/2009] [Indexed: 01/26/2023]
Abstract
Acute respiratory infections (ARIs) are a common reason for seeking medical attention, and the threat of pandemic influenza will likely add to these numbers. Using human viral challenge studies with live rhinovirus, respiratory syncytial virus, and influenza A, we developed peripheral blood gene expression signatures that distinguish individuals with symptomatic ARIs from uninfected individuals with >95% accuracy. We validated this "acute respiratory viral" signature-encompassing genes with a known role in host defense against viral infections-across each viral challenge. We also validated the signature in an independently acquired data set for influenza A and classified infected individuals from healthy controls with 100% accuracy. In the same data set, we could also distinguish viral from bacterial ARIs (93% accuracy). These results demonstrate that ARIs induce changes in human peripheral blood gene expression that can be used to diagnose a viral etiology of respiratory infection and triage symptomatic individuals.
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Affiliation(s)
- Aimee K Zaas
- Division of Infectious Diseases and International Health, Department of Medicine, Duke University School of Medicine, Duke University, Durham, NC 27710, USA
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