1
|
Mathisen M, Basnet S, Christensen A, Sharma AK, Tylden G, Krokstad S, Valentiner-Branth P, Strand TA. Viral and Atypical Bacterial Detection in Young Nepalese Children Hospitalized with Severe Pneumonia. Microbiol Spectr 2021; 9:e0055121. [PMID: 34704788 PMCID: PMC8549725 DOI: 10.1128/spectrum.00551-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/22/2021] [Indexed: 11/20/2022] Open
Abstract
Respiratory viruses cause a substantial proportion of respiratory tract infections in children but are underrecognized as a cause of severe pneumonia hospitalization in low-income settings. We employed 22 real-time PCR assays and retrospectively reanalyzed 610 nasopharyngeal aspirate specimens from children aged 2 to 35 months with severe pneumonia (WHO definition) admitted to Kanti Childrens' Hospital in Kathmandu, Nepal, from January 2006 through June 2008. Previously, ≥1 of 7 viruses had been detected by multiplex reverse transcription-PCR in 30% (188/627) of cases. Reanalyzing the stored specimens, we detected ≥1 pathogens, including 18 respiratory viruses and 3 atypical bacteria, in 98.7% (602/610) of cases. Rhinovirus (RV) and respiratory syncytial virus (RSV) were the most common, detected in 318 (52.1%) and 299 (49%) cases, respectively, followed by adenovirus (AdV) (10.6%), human metapneumovirus (hMPV) (9.7%), parainfluenza virus type 3 (8.4%), and enterovirus (7.7%). The remaining pathogens were each detected in less than 5%. Mycoplasma pneumoniae was most common among the atypical bacteria (3.7%). Codetections were observed in 53.3% of cases. Single-virus detection was more common for hMPV (46%) and RSV (41%) than for RV (22%) and AdV (6%). The mean cycle threshold value for detection of each pathogen tended to be lower in single-pathogen detections than in codetections. This finding was significant for RSV, RV, and AdV. RSV outbreaks occurred at the end of the monsoon or during winter. An expanded diagnostic PCR panel substantially increased the detection of respiratory viruses in young Nepalese children hospitalized with severe pneumonia. IMPORTANCE Respiratory viruses are an important cause of respiratory tract infections in children but are underrecognized as a cause of pneumonia hospitalization in low-income settings. Previously, we detected at least one of seven respiratory viruses by PCR in 30% of young Nepalese children hospitalized with severe pneumonia over a period of 36 months. Using updated PCR assays detecting 21 different viruses and atypical bacteria, we reanalyzed 610 stored upper-respiratory specimens from these children. Respiratory viruses were detected in nearly all children hospitalized for pneumonia. RSV and rhinovirus were the predominant pathogens detected. Detection of two or more pathogens was observed in more than 50% of the pneumonia cases. Single-virus detection was more common for human metapneumovirus and RSV than for rhinovirus and adenovirus. The concentration of virus was higher (low cycle threshold [CT] value) for single detected pathogens, hinting at a high viral load as a marker of clinical significance.
Collapse
Affiliation(s)
- Maria Mathisen
- Department of Medical Microbiology, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
| | - Sudha Basnet
- Department of Pediatrics, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Andreas Christensen
- Department of Medical Microbiology, St. Olav’s Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway
| | - Arun K. Sharma
- Department of Pediatrics, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Garth Tylden
- Department of Microbiology and Infection control, University Hospital of North Norway, Tromsø, Norway
| | - Sidsel Krokstad
- Department of Medical Microbiology, St. Olav’s Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Palle Valentiner-Branth
- Statens Serum Institut, Department of Infectious Disease Epidemiology and Prevention, Infectious Disease Preparedness, Copenhagen, Denmark
| | - Tor A. Strand
- Department of Research, Innlandet Hospital Trust, Lillehammer, Norway
| |
Collapse
|
2
|
Pérez-Sautu U, Wiley MR, Iglesias-Caballero M, Pozo F, Prieto K, Chitty JA, García-García ML, Calvo C, Casas I, Palacios G. Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology. Emerg Microbes Infect 2019; 8:1054-1065. [PMID: 31335277 PMCID: PMC6691886 DOI: 10.1080/22221751.2019.1640587] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Despite the advanced PCR-based assays available, a fraction of the pediatric respiratory infections remain unexplained every epidemic season, and there is a perception that novel viruses might be present in these specimens. We systematically collected samples from a prospective cohort of pediatric patients with respiratory infections, that returned negative results by validated molecular RT–PCR assays, and studied them with a target-independent, high-throughput sequencing-based approach. We also included a matched cohort of children with no symptoms of respiratory infection, as a contrast study population. More than fifty percent of the specimens from the group of patients with unexplained respiratory infections were resolved. However, the higher rate of detection was not due to the presence of novel viruses, but to the identification of well-known viral respiratory pathogens. Our results show that already known viral pathogens are responsible for the majority of cases that remain unexplained after the epidemic season. High-throughput sequencing approaches that use pathogen-specific probes are easier to standardize because they ensure reproducible library enrichment and sequencing. In consequence, these techniques might be desirable from a regulatory standpoint for diagnostic laboratories seeking to benefit from the many advantages of these sequencing technologies.
Collapse
Affiliation(s)
- Unai Pérez-Sautu
- a Influenza and Respiratory Viruses Unit, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII) , Madrid , Spain.,b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
| | - Michael Ross Wiley
- b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA.,c College of Public Health, University of Nebraska Medical Center , Omaha , NE , USA
| | - María Iglesias-Caballero
- a Influenza and Respiratory Viruses Unit, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
| | - Francisco Pozo
- a Influenza and Respiratory Viruses Unit, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
| | - Karla Prieto
- b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA.,c College of Public Health, University of Nebraska Medical Center , Omaha , NE , USA
| | - Joseph Alex Chitty
- b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
| | | | | | - Inmaculada Casas
- a Influenza and Respiratory Viruses Unit, National Center for Microbiology, Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
| | - Gustavo Palacios
- b Center for Genome Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID) , Frederick , MD , USA
| |
Collapse
|
3
|
Burgmeijer EH, Duijkers R, Lutter R, Bonten MJM, Schweitzer VA, Boersma WG. Plasma cytokine profile on admission related to aetiology in community-acquired pneumonia. CLINICAL RESPIRATORY JOURNAL 2019; 13:605-613. [PMID: 31310442 DOI: 10.1111/crj.13062] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 06/20/2019] [Accepted: 07/08/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND Potentially unnecessary antibiotic use for community-acquired pneumonia (CAP) contributes to selection of antibiotic-resistant pathogens. Cytokine expression at the time that treatment is started may assist in identifying patients not requiring antibiotics. We determined plasma cytokine patterns in patients retrospectively categorized as strict viral, pneumococcal or combined viral-bacterial CAP. OBJECTIVE To investigate whether cytokine-based prediction models can be used to differentiate strict viral CAP from other aetiologies at admission. METHODS From 344 hospitalized CAP patients, 104 patients were categorized as viral CAP (n = 17), pneumococcal CAP (n = 48) and combined bacterial-viral CAP (n = 39). IL-6, IL-10, IL-27, IFN-γ and C-reactive protein (CRP) were determined on admission in plasma. Prediction of strict viral aetiology was explored with two multivariate regression models and ROC curves. RESULTS Viral pneumonia was predicted by logistic regression using multiple cytokine levels (IL-6, IL-27 and CRP) with an AUC of 0.911 (95% CI: 0.852-0.971, P < .001). For the same patients the AUC of CRP was 0.813 (95% CI: 0.728-0.898, P < .001). CONCLUSIONS This study demonstrated differences in cytokine expression in selected CAP patients between viral and bacterial aetiology. Prospective validation studies are warranted.
Collapse
Affiliation(s)
- Eduard H Burgmeijer
- Department of Pulmonology, North West Hospital Alkmaar, Alkmaar, the Netherlands
| | - Ruud Duijkers
- Department of Pulmonology, North West Hospital Alkmaar, Alkmaar, the Netherlands
| | - René Lutter
- Departments of Respiratory Medicine and Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Marc J M Bonten
- Department of Molecular Epidemiology of Infectious diseases, Department of Medical Microbiology and Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Valentijn A Schweitzer
- Department of Molecular Epidemiology of Infectious diseases, Department of Medical Microbiology and Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Wim G Boersma
- Department of Pulmonology, North West Hospital Alkmaar, Alkmaar, the Netherlands
| |
Collapse
|
4
|
Serology Enhances Molecular Diagnosis of Respiratory Virus Infections Other than Influenza in Children and Adults Hospitalized with Community-Acquired Pneumonia. J Clin Microbiol 2016; 55:79-89. [PMID: 27795341 DOI: 10.1128/jcm.01701-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/06/2016] [Indexed: 02/06/2023] Open
Abstract
Both molecular and serological assays have been used previously to determine the etiology of community-acquired pneumonia (CAP). However, the extent to which these methods are correlated and the added diagnostic value of serology for respiratory viruses other than influenza virus have not been fully evaluated. Using data from patients enrolled in the Centers for Disease Control and Prevention (CDC) Etiology of Pneumonia in the Community (EPIC) study, we compared real-time reverse transcription-PCR (RT-PCR) and serology for the diagnosis of respiratory syncytial virus (RSV), human metapneumovirus (HMPV), parainfluenza virus 1 to 3 (PIV1, PIV2, and PIV3), and adenovirus (AdV) infections. Of 5,126 patients enrolled, RT-PCR and serology test results were available for 2,023, including 1,087 children below the age of 18 years and 936 adults. For RSV, 287 (14.2%) patients were positive by RT-PCR and 234 (11.6%) were positive by serology; for HMPV, 172 (8.5%) tested positive by RT-PCR and 147 (7.3%) by serology; for the PIVs, 94 (4.6%) tested positive by RT-PCR and 92 (4.6%) by serology; and for AdV, 111 (5.5%) tested positive by RT-PCR and 62 (3.1%) by serology. RT-PCR provided the highest number of positive detections overall, but serology increased diagnostic yield for RSV (by 11.8%), HMPV (by 25.0%), AdV (by 32.4%), and PIV (by 48.9%). The method concordance estimated by Cohen's kappa coefficient (κ) ranged from good (for RSV; κ = 0.73) to fair (for AdV; κ = 0.27). Heterotypic seroresponses observed between PIVs and persistent low-level AdV shedding may account for the higher method discordance observed with each of these viruses. Serology can be a helpful adjunct to RT-PCR for research-based assessment of the etiologic contribution of respiratory viruses other than influenza virus to CAP.
Collapse
|
5
|
Self WH, Williams DJ, Zhu Y, Ampofo K, Pavia AT, Chappell JD, Hymas WC, Stockmann C, Bramley AM, Schneider E, Erdman D, Finelli L, Jain S, Edwards KM, Grijalva CG. Respiratory Viral Detection in Children and Adults: Comparing Asymptomatic Controls and Patients With Community-Acquired Pneumonia. J Infect Dis 2015; 213:584-91. [PMID: 26180044 PMCID: PMC4721902 DOI: 10.1093/infdis/jiv323] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/22/2015] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The clinical significance of viruses detected in patients with community-acquired pneumonia (CAP) is often unclear. METHODS We conducted a prospective study to identify the prevalence of 13 viruses in the upper respiratory tract of patients with CAP and concurrently enrolled asymptomatic controls with real-time reverse-transcriptase polymerase chain reaction. We compared age-stratified prevalence of each virus between patients with CAP and controls and used multivariable logistic regression to calculate attributable fractions (AFs). RESULTS We enrolled 1024 patients with CAP and 759 controls. Detections of influenza, respiratory syncytial virus, and human metapneumovirus were substantially more common in patients with CAP of all ages than in controls (AFs near 1.0). Parainfluenza and coronaviruses were also more common among patients with CAP (AF, 0.5-0.75). Rhinovirus was associated with CAP among adults (AF, 0.93) but not children (AF, 0.02). Adenovirus was associated with CAP only among children <2 years old (AF, 0.77). CONCLUSIONS The probability that a virus detected with real-time reverse-transcriptase polymerase chain reaction in patients with CAP contributed to symptomatic disease varied by age group and specific virus. Detections of influenza, respiratory syncytial virus, and human metapneumovirus among patients with CAP of all ages probably indicate an etiologic role, whereas detections of parainfluenza, coronaviruses, rhinovirus, and adenovirus, especially in children, require further scrutiny.
Collapse
Affiliation(s)
- Wesley H Self
- Department of Emergency Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Derek J Williams
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | | | - James D Chappell
- Department of Pathology, Microbiology & Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | - Chris Stockmann
- Department of Pediatrics, University of Utah Health Sciences Center, Salt Lake City
| | - Anna M Bramley
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Dean Erdman
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lyn Finelli
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Seema Jain
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University School of Medicine, Nashville, Tennessee
| |
Collapse
|
6
|
Ho A. Viral pneumonia in adults and older children in sub-Saharan Africa - epidemiology, aetiology, diagnosis and management. Pneumonia (Nathan) 2014; 5:18-29. [PMID: 31641571 PMCID: PMC5922328 DOI: 10.15172/pneu.2014.5/446] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 06/27/2014] [Indexed: 01/14/2023] Open
Abstract
Community-acquired pneumonia causes substantial morbidity and mortality in sub-Saharan Africa with an estimated 131 million new cases each year. Viruses - such as influenza virus, respiratory syncytial virus and parainfluenza virus - are now recognised as important causes of respiratory disease in older children and adults in the developed world following the emergence of sensitive molecular diagnostic tests, recent severe viral epidemics, and the discovery of novel viruses. Few studies have comprehensively evaluated the viral aetiology of adult pneumonia in Africa, but it is likely to differ from Western settings due to varying seasonality and the high proportion of patients with immunosuppression and co-morbidities. Emerging data suggest a high prevalence of viral pathogens, as well as multiple viral and viral/bacterial infections in African adults with pneumonia. However, the interpretation of positive results from highly sensitive polymerase chain reaction tests can be challenging. Therapeutic and preventative options against viral respiratory infections are currently limited in the African setting. This review summarises the current state of the epidemiology, aetiology, diagnosis and management of viral pneumonia in sub-Saharan Africa.
Collapse
Affiliation(s)
- Antonia Ho
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Chichiri, Blantyre 3, Malawi
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| |
Collapse
|
7
|
Taboada B, Espinoza MA, Isa P, Aponte FE, Arias-Ortiz MA, Monge-Martínez J, Rodríguez-Vázquez R, Díaz-Hernández F, Zárate-Vidal F, Wong-Chew RM, Firo-Reyes V, del Río-Almendárez CN, Gaitán-Meza J, Villaseñor-Sierra A, Martínez-Aguilar G, Salas-Mier MDC, Noyola DE, Pérez-Gónzalez LF, López S, Santos-Preciado JI, Arias CF. Is there still room for novel viral pathogens in pediatric respiratory tract infections? PLoS One 2014; 9:e113570. [PMID: 25412469 PMCID: PMC4239085 DOI: 10.1371/journal.pone.0113570] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 10/24/2014] [Indexed: 11/30/2022] Open
Abstract
Viruses are the most frequent cause of respiratory disease in children. However, despite the advanced diagnostic methods currently in use, in 20 to 50% of respiratory samples a specific pathogen cannot be detected. In this work, we used a metagenomic approach and deep sequencing to examine respiratory samples from children with lower and upper respiratory tract infections that had been previously found negative for 6 bacteria and 15 respiratory viruses by PCR. Nasal washings from 25 children (out of 250) hospitalized with a diagnosis of pneumonia and nasopharyngeal swabs from 46 outpatient children (out of 526) were studied. DNA reads for at least one virus commonly associated to respiratory infections was found in 20 of 25 hospitalized patients, while reads for pathogenic respiratory bacteria were detected in the remaining 5 children. For outpatients, all the samples were pooled into 25 DNA libraries for sequencing. In this case, in 22 of the 25 sequenced libraries at least one respiratory virus was identified, while in all other, but one, pathogenic bacteria were detected. In both patient groups reads for respiratory syncytial virus, coronavirus-OC43, and rhinovirus were identified. In addition, viruses less frequently associated to respiratory infections were also found. Saffold virus was detected in outpatient but not in hospitalized children. Anellovirus, rotavirus, and astrovirus, as well as several animal and plant viruses were detected in both groups. No novel viruses were identified. Adding up the deep sequencing results to the PCR data, 79.2% of 250 hospitalized and 76.6% of 526 ambulatory patients were positive for viruses, and all other children, but one, had pathogenic respiratory bacteria identified. These results suggest that at least in the type of populations studied and with the sampling methods used the odds of finding novel, clinically relevant viruses, in pediatric respiratory infections are low.
Collapse
Affiliation(s)
- Blanca Taboada
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Marco A. Espinoza
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Pavel Isa
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Fernando E. Aponte
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | | | | | | | | | - Rosa María Wong-Chew
- Facultad de Medicina, Universidad Nacional Autónoma de México, México D.F., Mexico
| | | | | | - Jesús Gaitán-Meza
- Nuevo Hospital Civil de Guadalajara "Dr. Juan I. Menchaca", Guadalajara, Jalisco, Mexico
| | | | | | | | - Daniel E. Noyola
- Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | | | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Carlos F. Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
- * E-mail:
| |
Collapse
|
8
|
Houdouin V, Pouessel G, Angoulvant F, Brouard J, Derelle J, Fayon M, Ferroni A, Gangneux JP, Hau I, Le Bourgeois M, Lorrot M, Menotti J, Nathan N, Vabret A, Wallet F, Bonacorsi S, Cohen R, de Blic J, Deschildre A, Gandemer V, Pin I, Labbe A, Le Roux P, Martinot A, Rammaert B, Dubus JC, Delacourt C, Marguet C. Recommandations sur l’utilisation des nouveaux outils diagnostiques étiologiques des infections respiratoires basses de l’enfant de plus de trois mois. Arch Pediatr 2014; 21:418-23. [DOI: 10.1016/j.arcped.2014.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/16/2013] [Accepted: 01/23/2014] [Indexed: 10/25/2022]
|
9
|
Anderson TP, Werno AM, Barratt K, Mahagamasekera P, Murdoch DR, Jennings LC. Comparison of four multiplex PCR assays for the detection of viral pathogens in respiratory specimens. J Virol Methods 2013; 191:118-21. [PMID: 23583489 PMCID: PMC7119551 DOI: 10.1016/j.jviromet.2013.04.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 03/29/2013] [Accepted: 04/04/2013] [Indexed: 12/03/2022]
Abstract
This study will compare 4 different multiplex PCR assays. The xTAG RVP, Fast-track RP, Easyplex and an in-house rt-PCR assay were included. The performance of the assays was similar, with 93–100% agreement for comparisons. Non-performance aspects are key to deciding which of these assays to use.
Multiplex PCR has become the test of choice for the detection of multiple respiratory viruses in clinical specimens. However, there are few direct comparisons of different PCR assays. This study compares 4 different multiplex PCR assays for the recovery of common respiratory viruses. We tested 213 respiratory specimens using four different multiplex PCR assays: the xTAG respiratory viral panel fast (Abbott Molecular Laboratories), Fast-track Respiratory Pathogen assay (Fast-track Diagnostics), Easyplex respiratory pathogen 12 kit (Ausdiagnostics), and an in-house multiplex real-time PCR assay. The performance of the four assays was very similar, with 93–100% agreement for all comparisons. Other issues, such as through-put, technical requirements and cost, are likely to be as important for making a decision about which of these assays to use given their comparative performance.
Collapse
Affiliation(s)
- Trevor P Anderson
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | | | | | | | | | | |
Collapse
|
10
|
Planquette B, Ferré A, Bédos JP. [The role of atypical microorganisms and viruses in severe acute community-acquired pneumonia]. REANIMATION : JOURNAL DE LA SOCIETE DE REANIMATION DE LANGUE FRANCAISE 2013; 22:3-13. [PMID: 32288730 PMCID: PMC7117816 DOI: 10.1007/s13546-012-0634-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 11/21/2012] [Indexed: 11/26/2022]
Abstract
Usually, intensivists do not focus on atypical bacteria and viruses in severe community-acquired pneumonia (CAP). Only Legionella pneumophila and influenza virus, following the recent H1N1 influenza pandemic, are routinely suggested as responsible agents. However, CAP due to atypical bacteria may represent up to 44% of all CAP. Viral CAP is considered less severe than the usual bacterial ones, although 25% of them warrant hospitalization and 15% result in severe sepsis. Even though L. pneumophila is the most frequently atypical pathogen involved in severe cases, Mycoplasma pneumoniae may be responsible for multiorgan failure. To date, tools including detection of Legionella antigen in urine and Mycoplasma using polymerase chain reaction (PCR) allow rapid and accurate diagnosis. The treatment is based on macrolides and fluoroquinolones that can be associated in severe Legionnaire diseases. The presence of virus in CAP, either alone or in association with bacteria, has been demonstrated using molecular biology tests. These techniques also allowed the identification of several new viruses in CAP. However, the exact role of these detected viruses in CAP as well as the efficiency of antiviral therapy still represent major unsolved concerns.
Collapse
Affiliation(s)
- B. Planquette
- Service de réanimation médicochirurgicale, centre hospitalier de Versailles, site Mignot, 177, rue de Versailles, F-78150 Le Chesnay, France
| | - A. Ferré
- Service de réanimation médicochirurgicale, centre hospitalier de Versailles, site Mignot, 177, rue de Versailles, F-78150 Le Chesnay, France
| | - J. -P. Bédos
- Service de réanimation médicochirurgicale, centre hospitalier de Versailles, site Mignot, 177, rue de Versailles, F-78150 Le Chesnay, France
| |
Collapse
|
11
|
Murdoch DR, O'Brien KL, Driscoll AJ, Karron RA, Bhat N. Laboratory methods for determining pneumonia etiology in children. Clin Infect Dis 2012; 54 Suppl 2:S146-52. [PMID: 22403229 DOI: 10.1093/cid/cir1073] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Laboratory diagnostics are a core component of any pneumonia etiology study. Recent advances in diagnostic technology have introduced newer methods that have greatly improved the ability to identify respiratory pathogens. However, determining the microbial etiology of pneumonia remains a challenge, especially in children. This is largely because of the inconsistent use of assays between studies, difficulties in specimen collection, and problems in interpreting the presence of pathogens as being causally related to the pneumonia event. The laboratory testing strategy for the Pneumonia Etiology Research for Child Health (PERCH) study aims to incorporate a broad range of diagnostic testing that will be standardized across the 7 participating sites. We describe the current status of laboratory diagnostics for pneumonia and the PERCH approach for specimen testing. Pneumonia diagnostics are evolving, and it is also a priority of PERCH to collect and archive specimens for future testing by promising diagnostic methods that are currently under development.
Collapse
Affiliation(s)
- David R Murdoch
- Department of Pathology, University of Otago, Christchurch, New Zealand.
| | | | | | | | | | | | | |
Collapse
|
12
|
Bhat N, O'Brien KL, Karron RA, Driscoll AJ, Murdoch DR. Use and evaluation of molecular diagnostics for pneumonia etiology studies. Clin Infect Dis 2012; 54 Suppl 2:S153-8. [PMID: 22403230 PMCID: PMC3297547 DOI: 10.1093/cid/cir1060] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 12/21/2011] [Indexed: 01/16/2023] Open
Abstract
Comprehensive microbiological testing will be a core function of the Pneumonia Etiology Research for Child Health (PERCH) project. The development stage of PERCH provided the time and resources necessary for us to conduct a comprehensive review of the current state of respiratory diagnostics. These efforts allowed us to articulate the unique requirements of PERCH, establish that molecular methods would be central to our testing strategy, and focus on a short list of candidate platforms. This process also highlighted critical challenges in the general design and interpretation of diagnostic evaluation studies, particularly in the field of respiratory infections. Although our final molecular diagnostic platform was ultimately selected on the basis of operational and strategic considerations determined by the specific context of PERCH, our review highlighted several conceptual and practical challenges in respiratory diagnostics that have broader relevance for the performance and interpretation of pneumonia research studies.
Collapse
Affiliation(s)
- Niranjan Bhat
- Department of International Health, Johns Hopkins Bloomberg School of Public Health
- Division of Infectious Diseases, Department of Pediatrics, Johns Hopkins School of Medicine
| | | | - Ruth A. Karron
- Center for Immunization Research, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - David R. Murdoch
- Department of Pathology, University of Otago
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | | |
Collapse
|
13
|
Affiliation(s)
- Thomas M File
- Infectious Disease Section, Internal Medicine Department, Northeastern Ohio Universities College of Medicine and Pharmacy, Rootstown, OH 44272, USA.
| |
Collapse
|
14
|
Qiu F, Gu K, Yang B, Ding Y, Jiang D, Wu Y, Huang LL. DNA assay based on monolayer-barcoded nanoparticles for mass spectrometry in combination with magnetic microprobes. Talanta 2011; 85:1698-702. [PMID: 21807242 DOI: 10.1016/j.talanta.2011.06.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 06/14/2011] [Accepted: 06/15/2011] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) based methodology offers simple, fast and sensitive diagnosis. While it has become the predominate approach in biomolecular analysis, it has not been suitable for analyzing nucleic acid due to its low ionization efficiency. We report herein on a DNA assay based on monolayer-barcoded nanoparticles that were encoded with reporter mass molecules, which act as surrogate molecules for the matrix-assisted laser desorption/ionization time-of-flight MS (MALDI-TOF MS) identification of target DNA through mass spectrometry in combination with magnetic microprobes. This assay demonstrated high MS sensitivity, with the ability to detect target DNA at femtomolar (10(-15) M) levels. This inaugural effort using combined techniques is significant because it showed an extraordinary analytical capability for differentiating the single nucleotide polymorphism (SNP), which comprises the most abundant source of genetic variation in the human genome. We also report herein the feasibility of MS detection of two target DNAs that have the same mass but different nucleotide base composition, which classic MS methodology is inherently unable to differentiate.
Collapse
Affiliation(s)
- Fei Qiu
- Institute of Molecular Medicine, Huaqiao University, Quanzhou, PR China
| | | | | | | | | | | | | |
Collapse
|
15
|
Abstract
About 200 million cases of viral community-acquired pneumonia occur every year-100 million in children and 100 million in adults. Molecular diagnostic tests have greatly increased our understanding of the role of viruses in pneumonia, and findings indicate that the incidence of viral pneumonia has been underestimated. In children, respiratory syncytial virus, rhinovirus, human metapneumovirus, human bocavirus, and parainfluenza viruses are the agents identified most frequently in both developed and developing countries. Dual viral infections are common, and a third of children have evidence of viral-bacterial co-infection. In adults, viruses are the putative causative agents in a third of cases of community-acquired pneumonia, in particular influenza viruses, rhinoviruses, and coronaviruses. Bacteria continue to have a predominant role in adults with pneumonia. Presence of viral epidemics in the community, patient's age, speed of onset of illness, symptoms, biomarkers, radiographic changes, and response to treatment can help differentiate viral from bacterial pneumonia. However, no clinical algorithm exists that will distinguish clearly the cause of pneumonia. No clear consensus has been reached about whether patients with obvious viral community-acquired pneumonia need to be treated with antibiotics. Apart from neuraminidase inhibitors for pneumonia caused by influenza viruses, there is no clear role for use of specific antivirals to treat viral community-acquired pneumonia. Influenza vaccines are the only available specific preventive measures. Further studies are needed to better understand the cause and pathogenesis of community-acquired pneumonia. Furthermore, regional differences in cause of pneumonia should be investigated, in particular to obtain more data from developing countries.
Collapse
MESH Headings
- Adult
- Age Distribution
- Age Factors
- Antiviral Agents/therapeutic use
- Biomarkers/blood
- Child
- Community-Acquired Infections/diagnosis
- Community-Acquired Infections/epidemiology
- Community-Acquired Infections/virology
- Comorbidity
- Developing Countries/statistics & numerical data
- Diagnosis, Differential
- Global Health
- Humans
- Immunocompetence
- Lung/diagnostic imaging
- Lung/pathology
- Lung/virology
- Pandemics
- Pneumonia, Bacterial/diagnosis
- Pneumonia, Bacterial/epidemiology
- Pneumonia, Bacterial/microbiology
- Pneumonia, Bacterial/prevention & control
- Pneumonia, Viral/diagnosis
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/mortality
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/virology
- Radiography
- Specimen Handling
- United States/epidemiology
Collapse
Affiliation(s)
- Olli Ruuskanen
- Department of Paediatrics, Turku University Hospitals, Turku, Finland.
| | | | | | | |
Collapse
|
16
|
White S, Schultz T, Tufanaru C. The accuracy of Influenza A (H1N1) "swine flu" laboratory testing: A systematic review of diagnostic test accuracy. JBI LIBRARY OF SYSTEMATIC REVIEWS 2010; 8:1-21. [PMID: 27820051 DOI: 10.11124/01938924-201008081-00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Sarahlouise White
- 1 The Joanna Briggs Institute, Faculty of Health Sciences, the University of Adelaide, Adelaide 5005, Australia 2 Australian Patient Safety Foundation, Adelaide, SA 5005
| | | | | |
Collapse
|